Comparative Genomics Unveils the Habitat Adaptation and Metabolic Profiles of Clostridium in an Artificial Ecosystem for Liquor Production

Comparative genomic analysis of strain Priestia megaterium B1 reveals conserved potential for adaptation to endophytism and plant growth promotion

In our study, we aimed to explore the genomic and phenotypic traits of Priestia megaterium strain B1, which was isolated from root material of healthy apple plants, to adapt to the endophytic lifestyle and promote plant growth. We identified putative genes encoding proteins involved in chemotaxis, flagella biosynthesis, biofilm formation, secretory systems, detoxification, transporters, and transcription regulation. Furthermore, B1 exhibited both swarming and swimming motilities, along with biofilm formation. Both genomic and physiological analyses revealed the potential of B1 to promote plant growth through the production of indole-3-acetic acid and siderophores, as well as the solubilization of phosphate and zinc. To deduce potential genomic features associated with endophytism across members of P. megaterium strains, we conducted a comparative genomic analysis involving 27 and 31 genomes of strains recovered from plant and soil habitats, respectively, in addition to our strain B1. Our results indicated a closed pan genome and comparable genome size of strains from both habitats, suggesting a facultative host association and adaptive lifestyle to both habitats. Additionally, we performed a sparse Partial Least Squares Discriminant Analysis to infer the most discriminative functional features of the two habitats based on Pfam annotation. Despite the distinctive clustering of both groups, functional enrichment analysis revealed no significant enrichment of any Pfam domain in both habitats. Furthermore, when assessing genetic elements related to adaptation to endophytism in each individual strain, we observed their widespread presence among strains from both habitats. Moreover, all members displayed potential genetic elements for promoting plant growth.IMPORTANCEBoth genomic and phenotypic analyses yielded valuable insights into the capacity of P. megaterium B1 to adapt to the plant niche and enhance its growth. The comparative genomic analysis revealed that P. megaterium members, whether derived from soil or plant sources, possess the essential genetic machinery for interacting with plants and enhancing their growth. The conservation of these traits across various strains of this species extends its potential application as a bio-stimulant in diverse environments. This significance also applies to strain B1, particularly regarding its application to enhance the growth of plants facing apple replant disease conditions.

Monitoring longitudinal antimicrobial resistance trends of Staphylococcus aureus strains worldwide over the past 100 years to decipher its evolution and transmission

Staphylococcus aureus inhabits diverse habitats including food waste and wastewater treatment plants. Cases of S. aureus-induced infection are commonly reported worldwide. The emergence of antimicrobial resistance (AMR) of S. aureus is a growing public health threat worldwide. Here, we longitudinally monitored global trends in antibiotic resistance genes (ARGs) of 586 S. aureus strains, isolated between 1884 and 2022. The ARGs in S. aureus exhibited a significant increase over time (P < 0.0001). Mobile genetic elements play a crucial role in the transfer of ARGs in S. aureus strains. The structural equation model results revealed a significant correlation between the human development index and rising antibiotic consumption, which subsequently leads to an indirect escalation of AMR in S. aureus strains. Lastly, a machine learning algorithm successfully predicted the AMR risk of global terrestrial S. aureus with over 70% accuracy. Overall, these findings provided valuable insights for managing AMR in S. aureus.

Current situation, trend, and prospects of research on functional components from by-products of baijiu production: A review

In the present scenario marked by energy source shortages and escalating concerns regarding carbon dioxide emissions, there is a growing emphasis on the optimal utilization of biomass resources. Baijiu, as the Chinese national spirit, boasts remarkably high sales volumes annually. However, the production of baijiu yields various by-products, including solid residues (Jiuzao), liquid wastewater (Huangshui and waste alcohol), and gaseous waste. Recent years have witnessed dedicated research aimed at exploring the composition and potential applications of these by-products, seeking sustainable development and comprehensive resource utilization. This review systematically summarizes recent research, shedding light on both the baijiu brewing process and the bioactive compounds present baijiu production by-products (BPBPs). The primary focus lies in elucidating the potential extraction methods and applications of BPBPs, offering a practical approach to comprehensive utilization of by-products in functional food, medicine, cosmetic, and packaging fields. These applications not only contribute to enhancing production efficiency and mitigating environmental pollution, but also introduce innovative concepts for the sustainable advancement of associated industries. Future research avenues may include more in-depth compositional analysis, the development of utilization technologies, and the promotion of potential industrialization.

Comprehensive genomic and metabolomic analysis revealed the physiological characteristics and pickle like odor compounds metabolic pathways of Bacillus amyloliquefaciens ZZ7 isolated from fermented grains of Maotai-flavor baijiu

Pickle like odor (PLO) is one of the main defective flavors of Maotai flavor baijiu (MFB). Understanding and controlling the PLO compounds producing strains not only solves the problem of PLO from the source, but also ensures the high-quality production of MFB. However, the relevant research on PLO compounds producing strains has not been reported in MFB. In this study, we identified a Bacillus amyloliquefaciens ZZ7 with high yield of PLO compounds in the fermented grains of MFB, and measured its physiological characteristics. It produces 627 volatile compounds and 1,507 non-volatile compounds. There are 7 volatile sulfur compounds that cause the PLO, the content of dimethyl disulfide, dimethyl trisulfide, and dimethyl sulfur is relatively high, accounting for 89.43% of the total volatile sulfur compounds. The genome size of B. amyloliquefaciens ZZ7 is 3,902,720 bp with a GC content of 46.09%, and a total of 3,948 protein coding genes were predicted. Moreover, the functional annotation of coding genes and an assessment of the metabolic pathways were performed by genome annotation, showing it has strong ability to transport and metabolize amino acids and carbohydrates. Comprehensive genomic and metabolomic analysis, the metabolic pathway of PLO compounds of B. amyloliquefaciens ZZ7 was revealed, which mainly involves 12 enzymes including sulfate adenylyltransferase, cysteine synthase, cystathionine γ-synthase, etc. This work provides biological information support at both genetic and metabolic levels for the mechanism of B. amyloliquefaciens ZZ7 to synthesize PLO compounds, and provides a direction for the subsequent genetic modification of ZZ7 to solve PLO from the source in the MFB.

Microbial biogeography of pit mud from an artificial brewing ecosystem on a large time scale: all roads lead to Rome

IMPORTANCE

Baijiu is a typical example of how humans employ microorganisms to convert grains into new flavors. Mud cellars are used as the fermentation vessel for strong-flavor Baijiu (SFB) to complete the decomposition process of grains. The typical flavor of SFB is mainly attributed to the metabolites of the pit mud microbiome. China has a large number of SFB-producing regions. Previous research revealed the temporal profiles of the pit mud microbiome in different geographical regions. However, each single independent study rarely yields a thorough understanding of the pit mud ecosystem. Will the pit mud microbial communities in different production regions exhibit similar succession patterns and structures under the impact of the brewing environment? Hence, we conducted research in pit mud microbial biogeography to uncover the impact of specific environment on the microbial community over a long time scale.

Succession of microbial community of the pit mud under the impact of Daqu of Nongxiang Baijiu

Complex microbiomes of pit mud play significant roles in imbuing flavors and qualities of Nongxiang Baijiu during fermentation. However, pit mud microbial enrichment and succession is a long process that is also accompanied by aging. Development of high-quality artificial pit mud becomes an urgent problem. In this study, a new medium based on space (TK) Daqu was used to effectively enrich the dominant microorganisms in pit mud. The results showed that Caproiciproducens was the most preponderance in the cultures unadded Daqu, whereas Clostridium sensu stricto 12 was the most preponderance, followed by Caproiciproducens in the enrichment cultures added TK Daqu. It is worth noting that TK Daqu balanced the relative abundance of Caproiciproducens and Clostridium sensu stricto 12 in 100-year pit mud culture (S100), which was more conducive to the increase of methanogens. PICRUSt2 prediction results showed that hydrogenotrophic methanogens could promote the synthesis of caproic acid by using the product H2 as the metabolic substrate and increased significantly in the pit mud enrichment cultures with TK Daqu. The increase of lactate dehydrogenase (EC 1.1.1.27) content in S100 contributed to the degradation of lactic acid and the increase of caproic acid. Adding TK Daqu enrichment cultures is more conducive to the enrichment and metabolic balance of pit mud microorganisms.

Monitoring Longitudinal Trends and Assessment of the Health Risk of Shigella flexneri Antimicrobial Resistance

Shigella flexneri infection is the main cause of diarrhea in humans worldwide. The emergence of antimicrobial resistance (AMR) of S. flexneri is a growing public health threat worldwide, while large-scale studies monitoring the longitudinal AMR trends of isolates remain scarce. Here, the AMR gene (ARG) profiles of 717 S. flexneri isolates from 1920 to 2020 worldwide were determined. The results showed that the average number of ARGs in isolates has increased significantly, from 19.2 ± 2.4 before 1970 to 29.6 ± 5.3 after 2010. In addition, mobile genetic elements were important contributors to ARGs in S. flexneri isolates. The results of the structural equation model showed that the human development index drove the consumption of antibiotics and indirectly promoted the antibiotic resistance. Finally, a machine learning algorithm was used to predict the antibiotic resistance risk of global terrestrial S. flexneri isolates and successfully map the antibiotic resistance threats in global land habitats with over 80% accuracy. Collectively, this study monitored the longitudinal AMR trends, quantitatively surveilled the health risk of S. flexneri AMR, and provided a theoretical basis for mitigating the threat of antibiotic resistance.

Chemotaxis of Clostridium Strains Isolated from Pit Mud and Its Application in Baijiu Fermentation

Clostridium is the key bacteria that inhabits the pit mud in a fermentation cell, for the production of strong-flavor Baijiu. Its activities in the process of Baijiu fermentation is closely related to the niches of pit mud and cells. After multiple rounds of underground fermentation, Clostridium has been domesticated and adapted to the environment. The mechanisms of clostridia succession in the pit mud and how they metabolize nutrients present in grains are not clear. In this study, 15 Clostridium species including three firstly reported ones (Clostridium tertium, Clostridium pabulibutyricum and Clostridium intestinale) in strong-flavor Baijiu pit mud, were isolated from the pit mud. Eighty one percent of these Clostridium strains are motile, and most of them show chemotaxis to organic acids, glutathione, saccharides and lactic acid bacteria. In a simulated Baijiu fermentation system, Clostridium migrated from pit mud to fermented grains with the addition of chemokine lactic acid, resulting in the production of acetic acid and butyric acid. The results help to understand the succession mechanism of Clostridium in pit mud, and provide a reference for regulation of lactic acid level in fermented grains during Baijiu fermentation.

Effects of post-fermentation on the flavor compounds formation in red sour soup

Red Sour Soup (RSS) is a traditional fermented food in China. After two rounds of fermentation, sour soup has a mellow flavor. However, the microbial composition and flavor formation processes in post-fermentation in RSS are unclear. This study investigates the bacteria composition of RSS during the post-fermentation stage (0–180 days) using high-throughput sequencing. The results show that lactic acid bacteria (LAB) are dominant during the post-fermentation process, and their abundance gradually increases with fermentation time. Additionally, gas chromatography-mass spectrometry was used to detect volatile flavor compounds in the post-fermentation process. Seventy-seven volatile flavor compounds were identified, including 24 esters, 14 terpenes, 9 aromatic hydrocarbons, 9 alkanes, 6 heterocyclic compounds, 3 alcohols, 3 acids, 3 ketones, 2 phenols, 2 aldehydes, 1 amine, and 1 other. Esters and aromatic hydrocarbons are the main volatile compounds in RSS during the post-fermentation process. Orthogonal partial least squares screening and correlation analysis derived several significant correlations, including 48 pairs of positive correlations and 19 pairs of negative correlations. Among them, Acetobacter spp., Clostridium spp. and Sporolactobacillus spp. have 15, 14, 20 significant correlation pairs, respectively, and are considered the most important bacterial genera post-fermentation. Volatile substances become abundant with increasing fermentation time. LAB are excessive after more than 120 days but cause a drastic reduction in volatile ester levels. Thus, the post-fermentation time should be restricted to 120 days, which retains the highest concentrations of volatile esters in RSS. Overall, these findings provide a theoretical basis to determine an optimal post-fermentation time duration, and identify essential bacteria for manufacturing high-quality starter material to shorten the RSS post-fermentation processing time.