Reference gene catalog and metagenome-assembled genomes from the gut microbiome reveal the microbial composition, antibiotic resistome, and adaptability of a lignocellulose diet in the giant panda.

The giant panda, a strict herbivore that feeds on bamboo, still retains a typical carnivorous digestive system. Reference catalogs of microbial genes and genomes are lacking, largely limiting the antibiotic resistome and functional exploration of the giant panda gut microbiome. Here, we integrated 177 fecal metagenomes of captive and wild giant pandas to construct a giant panda integrated gene catalog (GPIGC) comprised of approximately 4.5 million non-redundant genes and reconstruct 393 metagenome-assembled genomes (MAGs). Taxonomic and functional characterization of genes revealed that the captivity of the giant panda significantly changed the core microbial composition and the distribution of microbial genes. Higher abundance and prevalence of antibiotic resistance genes (ARGs) were detected in the guts of captive giant pandas, and ARG distribution was influenced by geography, for both captive and wild individuals. Escherichia, as the prevalent genus in the guts of captive giant pandas, was the main carrier of ARGs, meaning there is a high risk of ARG transmission by Escherichia. We also found that multiple mcr gene variants, conferring plasmid-mediated mobile colistin resistance, were widespread in the guts of captive and wild giant pandas. There were low proportions of carbohydrate-active enzyme (CAZyme) genes in GPIGC and MAGs compared with several omnivorous and herbivorous mammals. Many members of Clostridium MAGs were significantly enriched in the guts of adult, old and wild giant pandas. The genomes of isolates and MAGs of Clostridiaceae harbored key genes or enzymes in complete pathways for degrading lignocellulose and producing short-chain fatty acids (SCFAs), indicating the potential of these bacteria to utilize the low-nutrient bamboo diet. Overall, our data presented an exhaustive reference gene catalog and MAGs in giant panda gut and provided a comprehensive understanding of the antibiotic resistome and microbial adaptability for a high-lignocellulose diet.

Developing defined starter culture for reproducible profile of flavour compound in Chinese xiaoqu baijiu fermentation.

Defined starter cultures, containing selected microbes could reduce the complexity of natural starter, are beneficial for controllable food fermentations. However, there are challenges in identifying key microbiota and constructing synthetic microbiota for traditional food fermentations. Here, we aimed to develop a defined starter culture for reproducible profile of flavour compounds, using Chinese Xiaoqu Baijiu fermentation as a case. We classified all microbes into 4 modules using weighted correlation network analysis. Module 3 presented significant correlations with flavour compounds (P < 0.05) and the highest gene abundance related with flavour compound production. 13 dominant species in module 3 were selected for mixed culture fermentation, and each species was individually deleted to analyse the effect on flavour compound production. Ten species, presenting significant effects (P < 0.05) on flavour compound production, were selected for developing the starter culture, including Rhizopus oryzae, Rhizopus microsporus, Saccharomyces cerevisiae, Pichia kudriavzevii, Wickerhamomyces anomalus, Lactobacillus acetotolerans, Levilactobacillus brevis, Weissella paramesenteroides, Pediococcus acidilactici, and Leuconostoc pseudomesenteroides. After optimising the structure of the starter culture, the profile similarity of flavour compounds produced by the starter culture reached 81.88% with that by the natural starter. This work indicated feasibility of reproducible profile of flavour compounds with defined starter culture for food fermentations.

Insights into antibiotic and heavy metal resistance interactions in Escherichia coli isolated from livestock manure and fertilized soil.

Heavy metal and antibiotic-resistant bacteria from livestock feces are ecological and public health problems. However, the distribution and relationships of antibiotic resistance genes (ARGs), heavy metal resistance genes (HMRGs), and virulence factors (VFs) and their transmission mechanisms remain unclear. Therefore, we investigated the resistance of Escherichia coli, the prevalence of its ARGs, HMRGs, and VFs, and their transmission mechanisms in livestock fresh feces (FF), composted feces (CF), and fertilized soil (FS). In total, 99.54% (n = 221) and 91.44% (n = 203) of E. coli were resistant to at least one antibiotic and one heavy metal, respectively. Additionally, 72.52% (n = 161) were multi-drug resistant (MDR), of which Cu-resistant E. coli accounted for 72.67% (117/161). More than 99.34% (88/89) of E. coli carried multidrug ARGs, VFs, and the Cu resistance genes cueO and cusABCRFS. The Cu resistance genes cueO and cusABCRFS were mainly located on chromosomes, and cueO and cusF were positively associated with HMRGs, ARGs, and VFs. The Cu resistance genes pcoABCDRS were located on the plasmid pLKYL-P02 flanked by ARGs in PF18C from FF group and on chromosomes flanked by HMRGs in SAXZ1-1 from FS group. These results improved our understanding of bacterial multidrug and heavy metal resistance in the environment.

AIM2 participates in house dust mite (HDM)-induced epithelial dysfunctions and ovalbumin (OVA)-induced allergic asthma in infant mice.

Objective: Allergen sensitization and high rates of concomitant allergic diseases are characteristic of severe pediatric asthma. The present study was aimed to explore the mechanism of allergic asthma via bioinformatics and experiment investigation.Methods: The GSE27011 dataset contained the expression profiles of normal and pediatric asthma white blood cells was downloaded for analyzing the different expression genes and function enrichment. The allergic asthma model in infant mice was established by ovalbumin (OVA) stimulation. The cellular model was established by house dust mite (HDM)-stimulation in human bronchial epithelial cells. The absent in melanoma 2 (AIM2) knockdown was achieved by intranasal lentivirus injection or cell infection. The bronchoalveolar lavage fluid (BALF) was collected for cell counting and ELISA assessment of cytokines. Lung tissues were collected for HE staining and immunohistochemical (IHC) staining. Real-time PCR and immunoblotting were used for the determination of key gene expressions in mouse and cell models.Results: upregulation of AIM2 gene expression was observed in pediatric asthma patients based on GSE27011 and OVA-induced infant mouse allergic asthma model. AIM2 knockdown ameliorated OVA caused elevation in airway hyper-responsiveness (AHR), elevation in cell quantities (eosinophils, neutrophils, lymphocytes), and levels of cytokines (IL-4, IL-13, TNF-α, and OVA-specific IgE) in BALF. Moreover, AIM2 knockdown relieved OVA-caused histopathological alterations in mouse lungs, up-regulation of AIM2 levels, and NOD1 and receptor-interacting protein 2 (RIP2) protein levels, as well as p65 phosphorylation. In the cell model, AIM2 knockdown partially ameliorated HDM-induced epithelial dysfunctions by promoting cell viability, down-regulating inflammatory cytokines levels, and decreasing the protein levels of AIM2, NOD1, RIP2, and phosphorylated p65.Conclusion: AIM2 participates in HDM-induced epithelial dysfunctions and OVA-induced allergic asthma progression. AIM2 could be a promising target for pediatric allergic asthma treatment regimens, which warrants further in vivo investigations.

Effects of environmental disinfection on microbial population and resistance genes: A case study of the microecology within a panda enclosure.

Widespread use of disinfectants raises concerns over their involvement in altering microbial communities and promoting antimicrobial resistance. This study explores the influence of disinfection protocols on microbial populations and resistance genes within an isolated enclosure environment and in the gut of giant pandas (GPs) held within. Samples of panda feces, air conditioning ducts, soil and bamboo were collected before and after disinfection. High-throughput sequencing characterized the microbial flora of GP gut and environmental microbes inside the artificial habitat. Microbial cultures showed that Escherichia coli (34.6%), Enterococcus (15.4%) and other pathogenic bacteria deposited in feces and the enclosure. Isolates exhibit a consistent resistance to disinfectant, with the greatest resistance shown to cyanuric acid, and the lowest to glutaraldehyde-dodecyl dimethyl ammonium bromide (GD-DDAB) and dodecyl dimethyl ammonium bromide (DDAB). The total number of the culturable bacteria in soil and bamboo were significantly diminished after disinfection but increased in the gut. After disinfection, the richness (Chao1 index) of environment samples increased significantly (P < 0.05), while the richness in gut decreased significantly (P < 0.05). Ten genera showed significant change in feces after disinfection. Metagenome sequencing showed that 126 types of virulence genes were present in feces before disinfection and 37 in soil. After disinfection, 110 virulence genes localized in feces and 53 in soil. Eleven virulence genes including ECP and T2SS increased in feces. A total of 182 antibiotic resistance genes (ARGs) subtypes, potentially conferring resistance to 20 classes of drugs, were detected in the soils and feces, with most belonging to efflux pump protein pathways. After disinfection, the number of resistance genes increased both in gut and soil, which suggests disinfection protocols increase the number of resistance pathways. Our study shows that the use of disinfectants helps to shape the microbial community of GPs and their habitat, and increases populations of resistant strain bacteria.

Gut microbiota enhance energy accumulation of black-necked crane to cope with impending migration.

Less is known about the role of gut microbiota in overwintering environmental adaptation in migratory birds. Here, we performed metagenomic sequencing on fresh fecal samples (n = 24) collected during 4 periods of overwintering (Dec: early; Jan: middle I; Feb: middle II; Mar: late) to characterize gut microbial taxonomic and functional characteristics of black-necked crane (Grus nigricollis). The results demonstrated no significant change in microbial diversity among overwintering periods. Analysis of compositions of microbiomes with bias correction (ANCOM-BC) determined 15 Proteobacteria species enriched in late overwintering period. Based on previous reports, these species are associated with degradation of chitin, cellulose, and lipids. Meanwhile, fatty acid degradation and betalain biosynthesis pathways are enriched in late overwintering period. Furthermore, metagenomic binning obtained 91 high-quality bins (completeness >70% and contamination <10%), 5 of which enriched in late overwintering period. Carnobacterium maltaromaticum, unknown Enterobacteriaceae, and Yersinia frederiksenii have genes for chitin and cellulose degradation, acetate, and glutamate production. Unknown Enterobacteriaceae and Y. frederiksenii hold genes for synthesis of 10 essential amino acids required by birds, and the latter has genes for γ-aminobutyrate production. C. maltaromaticum has genes for pyridoxal synthesis. These results implied the gut microbiota is adapted to the host diet and may help black-necked cranes in pre-migratory energy accumulation by degrading the complex polysaccharide in their diet, supplying essential amino acids and vitamin pyridoxal, and producing acetate, glutamate, and γ-aminobutyrate that could stimulate host feeding. Additionally, enriched Proteobacteria also encoded more carbohydrate-active enzymes (CAZymes) and antibiotic resistance genes (ARGs) in late overwintering period. KEY POINTS: • Differences in gut microbiota function during overwintering period of black-necked cranes depend mainly on changes in core microbiota abundance • Gut microbiota of black-necked crane adapted to the diet during overwintering period • Gut microbiota could help black-necked cranes to accumulate more energy in the late overwintering period.

The Fecal and Serum Metabolomics of Giant Pandas Based on Untargeted Metabolomics.

Little is comprehensively known or understood about giant panda fecal and serum metabolites, which could serve as important indicators of the physiological metabolism of giant pandas. Therefore, we determined the contents of fecal and serum metabolites of giant pandas based on an untargeted metabolome. Four hundred and 955 metabolites were detected in the feces and serum of giant panda, respectively. Glycerophospholipid and choline metabolism were the main metabolic pathways in feces and serum. A significant correlation between the gut microbiota and fecal metabolites was found (P < 0.01). Fecal metabolites were not greatly affected by the age or gender of giant pandas, but serum metabolites were significantly affected by age and gender. The majority of different metabolites caused by age were higher in serum of younger giant pandas, including fatty acids, lipids, metabolites of bile acids, and intermediate products of vitamin D3. The majority of different metabolites caused by gender included fatty acids, phosphatidylcholine (PC), phosphatidylserine (PS), and phosphatidylethanolamine (PE). A separate feeding diet should be considered according to different ages and genders of giant panda. Therefore, our results could provide helpful suggestions to further protect captive giant pandas.

Heavy metals, antibiotics and nutrients affect the bacterial community and resistance genes in chicken manure composting and fertilized soil.

Succession of bacterial communities involved in the composting process of chicken manure, including first composting (FC), second composting (SC) and fertilizer product (Pd) and fertilized soil (FS), and their associations with nutrients, heavy metals, antibiotics and antibiotic resistance genes (ARGs) were investigated. Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria were the dominant phyla observed during composting. Overall, potential pathogenic bacteria decreased from 37.18% (FC) to 3.43% (Pd) and potential probiotic taxa increased from 5.77% (FC) to 7.12% (Pd). Concentrations of heavy metals increased after second composting (SC), however, no significant differences were observed between FS and CS groups. Alpha diversities of bacterial communities showed significant correlation with heavy metals and nutrients. All investigated antibiotics decreased significantly after the composting process. The certain antibiotics, heavy metals, or nutrients was significantly positive correlated with the abundance of ARGs, highlighting that they can directly or indirectly influence persistence of ARGs. Overall, results indicated that the composting process is effective for reducing potential pathogenic bacteria, antibiotics and ARGs. The application of compost lead to a decrease in pathogens and ARGs, as well as an increase in potentially beneficial taxa and nutrients in soil.

Wideband Spectrum Sensing Based on Riemannian Distance for Cognitive Radio Networks.

Detecting the signals of the primary users in the wideband spectrum is a key issue for cognitive radio networks. In this paper, we consider the multi-antenna based signal detection in a wideband spectrum scenario where the noise statistical characteristics are assumed to be unknown. We reason that the covariance matrices of the spectrum subbands have structural constraints and that they describe a manifold in the signal space. Thus, we propose a novel signal detection algorithm based on Riemannian distance and Riemannian mean which is different from the traditional eigenvalue-based detector (EBD) derived with the generalized likelihood ratio criterion. Using the moment matching method, we obtain the closed expression of the decision threshold. From the considered simulation settings, it is shown that the proposed Riemannian distance detector (RDD) has a better performance than the traditional EBD in wideband spectrum sensing.

Antibiotic and disinfectant resistance of Salmonella isolated from egg production chains.

To investigate the contamination of Salmonella and its drug resistance in egg production chains, 111 Salmonella strains of different serotypes isolated from egg production chains were used in the study. The minimum inhibitory concentrations (MICs) of antibiotics and disinfectants against Salmonella isolates were determined, meanwhile, antibiotic and disinfectant resistance genes were amplified. The results showed that the resistance frequency of trimethoprim (TMP, N=100, P=90.09%) was highest among Salmonella isolates and all isolates were sensitive to amoxicillin and clavulanate (AMC), ceftiofur sodium (CFS) and gentamicin (CN), respectively. There were six different antibiotic resistance profiles, and TMP profile was the most prevalent type (N=36, P=32.43%). 52.25% of Salmonella isolates appeared multi-drug resistance. The MICs of benzalkonium chloride (BC) and cetylpyridinium chloride (CPC) against Salmonella strains ranged from 8 to 128 µg/mL and 8 to 256 µg/mL, respectively. Compared to quality control strain Escherichia coli ATCC10536, 101 Salmonella isolates (P=90.99%) had dual resistances to BC and CPC. 109 Salmonella (P=98.20%) were co-resistant to antibiotic and disinfectant. Detection of drug resistance genes showed that blaTEM gene was dominant (N=49, P=44.14%). The qnrA, qnrB and qepA genes were not detected. Only qacEΔ1 gene (N=63, P=56.76%) was detected among the disinfectant resistance genes. There was a significant correlation between sul1 gene and qacEΔ1 gene (P < 0.01). S. Derby showed multi-resistances to TMP, oxytetracycline (OTC), amoxicillin (AML) and ciprofloxacin (CIP). Eleven antibiotic resistance genes were found in S. Derby, in which the prevalence of qacEΔ1 gene was 81.25% (N=52). Besides, the drug resistance frequency and the prevalence of drug resistance genes in internal farm environment were higher than those in external environment. High frequency of drug resistances and high prevalence of drug resistance genes were detected in all links of the egg production chains, including package, storage and sale. Our results showed that severe antibiotic and disinfectant resistances existed in egg production chains. Therefore, further hygiene supervision should be implemented to prevent and control Salmonella, and standardize the use of antibiotics and disinfectants.

Evolution of self-assembled amphiphilic colloidal particles in strong-flavor Chinese baijiu.

This study proposed the evolution of self-assembled amphiphilic colloidal particles in Strong-Flavor (SF) Baijiu based on Ostwald ripening for the first time. The evolution process occurs in two stages: disordered amphiphilic molecules self-assemble into small colloidal particles and subsequently undergo Oswald ripening to form larger hydrophobic particles. Microscopic observations revealed the average size of oil-like spherical colloidal particles in Baijiu increased from 1.86 µm to 2.96 µm while the number of particles decreased by 39.50% during the 16-year cellaring process of SF Baijiu, consistent with the particle size trend observed via laser scattering. During fusion process, the charge-to-mass ratio of positively charged colloidal particles decreased, leading ζ-potential decreased from 23.7 mV to 4.66 mV within 16 years of storage. The electrochemical impedance spectroscopy approach tracked the unidirectional variation in the dielectric constant during evolution of SF Baijiu, reflecting the gradual expansion of colloidal particles, which aligns with the evolution trend observed in molecular dynamics simulations. By integrating direct microscopic observations of amphiphilic colloidal particles with electrochemical techniques, the evolution of Baijiu samples is capable to be evaluated in-situ, laying the foundation for intelligent Baijiu aging monitoring technology.

Compound heterozygous B3GALNT2 mutations in a fetus with encephalocele: A case report.

An encephalocele is a congenital malformation characterized by protrusion of the intracranial contents through a cranial defect. We report that a fetus of a pregnant mother who had two consecutive pregnancies with ultrasound-detected encephalocele carried compound heterozygous variants in B3GALNT2 NM_152490.5:c.[1423C > T (p.Gln475Ter)]; [261-2A > G] of maternal and paternal origins, respectively, as confirmed by exome sequencing followed by Sanger sequencing validation. The present case implies that mutations in B3GALNT2, a well-known dystroglycanopathy causative gene, may result in a phenotype of neural tube defect, providing new insights into the clinical spectrum of B3GALNT2-related disorders. Our study may contribute to prenatal screening/diagnosis and genetic counseling of congenital brain malformations.

Antimicrobial resistance spectrum and virulence characterization of Escherichia coli, Klebsiella pneumoniae and Proteus mirabilis isolated from asymptomatic and diarrheal rhesus monkeys.

This study aims to deepen our understanding of the drug resistance and virulence characterization among gut bacteria in asymptomatic and diarrheal captive rhesus macaques (RMs). A total of 31 samples, including 8 asymptomatic RMs, 10 diarrheal RMs, and 1 dead RM, were collected from a breeding base in Sichuan, China, for bacterial isolation. As a result, Escherichia coli (n = 23), Klebsiella (n = 22), Proteus mirabilis (n = 10), Enterococcus (n = 10), Salmonella (n = 2), and Staphylococcus (n = 2) were isolated. All isolates were subjected to antimicrobial susceptibility testing and whole-genome sequencing, among which some E. coli, K. pneumoniae, and P. mirabilis were subjected to the Galleria mellonella and mice infection testing. The antimicrobial resistance rates of levofloxacin, enrofloxacin, and cefotaxime in diarrhea-associated isolates were higher than those of asymptomatic isolates. Consistent with the antimicrobial resistance phenotype, diarrheal isolates had a higher prevalence rate to qnrS1, blaTEM-1B and blaCTX-M-27 than asymptomatic isolates. Furthermore, compared with asymptomatic isolates, diarrheal isolates demonstrated a higher pathogenic potential against larvae and mice. Additionally, sequence types (STs) 14179-14181 in E. coli and ST 625 and ST 630-631 in Klebsiella aerogenes were firstly characterized. Our evidence underscores the considerable challenge posed by high rates of bacterial drug resistance in the effective treatment of diarrheal RMs.

Epidemiological investigation of Entamoeba in wild rhesus macaques in China: A novel ribosomal lineage and genetic differentiation of Entamoeba nuttalli.

Wild rhesus macaques are a potential source of zoonotic parasites for humans, and Entamoeba spp. are common intestinal parasites. To investigate the prevalence of Entamoeba in wild rhesus macaques in China and explore the genetic differentiation of the potentially pathogenic species Entamoeba nuttalli, a total of 276 fecal samples from five populations at high altitudes (HAG, 2,800-4,100 m above sea level) and four populations at low altitudes (LAG, 5-1,000 m above sea level) were collected. PCR methods based on the ssrRNA gene were used to detect Entamoeba infection. Genotyping of E. nuttalli was performed based on six tRNA-linked short tandem repeat (STR) loci for further genetic analyses. The results revealed that Entamoeba infection (69.2%) was common in wild rhesus macaques in China, especially in LAG which had a significantly higher prevalence rate than that in HAG (P < 0.001). Three zoonotic species were identified: Entamoeba chattoni (60.9%) was the most prevalent species and distributed in all the populations, followed by Entamoeba coli (33.3%) and Entamoeba nuttalli (17.4%). In addition, a novel Entamoeba ribosomal lineage named RL13 (22.8%) was identified, and phylogenetic analysis revealed a close genetic relationship between RL13 and Entamoeba. hartmanni. Genotyping of E. nuttalli obtained 24 genotypes from five populations and further analysis showed E. nuttalli had a high degree of genetic differentiation (FST > 0.25, Nm < 1) between the host populations. The result of analysis of molecular variance (AMOVA) revealed that observed genetic differences mainly originate from differences among populations (FST = 0.91). Meanwhile, the phylogenetic tree showed that these genotypes of E. nuttalli were clustered according to geographical populations, indicating a significant phylogeographic distribution pattern. Considering the potential pathogenicity of E. nuttalli, attention should be paid to its risk of zoonotic transmission.

Deciphering the microbial succession and color formation mechanism of "green-covering and red-heart" Guanyin Tuqu.

"Green-covering and red-heart" Guanyin Tuqu (GRTQ), as a type of special fermentation starter, is characterized by the "green-covering" formed on the surface of Guanyin Tuqu (SQ) and the "red-heart" in the center of Guanyin Tuqu (CQ). However, the mechanisms that promote temporal succession in the GRTQ microbial ecology and the formation of "green-covering and red-heart" characteristics remain unclear. Herein, we correlated the temporal profiles of microbial community succession with the main environmental variables (temperature, moisture, and acidity) and spatial position (center and surface) in GRTQ throughout fermentation. According to the results of high-throughput sequencing and culture-dependent methods, the microbial communities in the CQ and SQ demonstrated functional complementarity. For instance, the bacterial richness index of the CQ was greater than that of SQ, and the fungal richness index of the SQ was greater than that of CQ at the later stage of fermentation. Furthermore, Saccharomycopsis, Saccharomyces, Aspergillus, Monascus, Lactobacillus, Bacillus, Rhodanobacter, and Chitinophaga were identified as the dominant microorganisms in the center, while the surface was represented by Saccharomycopsis, Aspergillus, Monascus, Lactobacillus, Acetobacter, and Weissella. By revealing the physiological characteristics of core microorganisms at different spatial positions of GRTQ, such as Aspergillus clavatus and Monascus purpureus, as well as their interactions with environmental factors, we elucidated the color formation mechanism behind the phenomenon of "green" outside and "red" inside. This study provides fundamental information support for optimizing the production process of GRTQ.

Aroma Compound Changes in the Jiangxiangxing Baijiu Solid-State Distillation Process: Description, Kinetic Characters and Cut Point Selection.

Solid-state distillation is a distinctive process for extracting the baijiu aroma compounds that determine the flavor character of baijiu. In this study, the changes in various chemical properties of the aroma compounds in three classical Jiangxiangxing baijiu fermented grain distillation processes were analyzed. The changes in the aroma compounds in the instantaneous distillates were quantified and correlation analyzes were conducted. The results showed that the effect of the aroma compounds was greater than the differences between the fermented grains. Eleven representative aroma compounds were selected to develop the kinetic models describing two opposing changes. For the regulation of the Jiangxiangxing baijiu aroma compounds, their recovery rates were calculated using a kinetic model. A comprehensive comparison of the recovery rates of the characteristic aroma and other aroma compounds at different cut-off values revealed that the optimum recovery rate of the characteristic aroma of Jiangxiangxing baijiu 2,3,5,6-tetramethylpyrazine was 14.53% at cut-off values of 3.9 and 19.8 min. In this study, representative changes in the aroma compounds and the selection of cut-off values to regulate the baijiu distillation aroma were proposed.

Core microbes identification and synthetic microbiota construction for the production of Xiaoqu light-aroma Baijiu.

Baijiu production has relied on natural inoculated Qu as a starter culture, causing the unstable microbiota of fermentation grains, which resulted in inconsistent product quality across batches. Therefore, revealing the core microbes and constructing a synthetic microbiota during the fermentation process was extremely important for stabilizing product quality. In this study, the succession of the microbial community was analyzed by high-throughput sequencing technology, and ten core microbes of Xiaoqu light-aroma Baijiu were obtained by mathematical statistics, including Acetobacter, Bacillus, Lactobacillus, Weissella, Pichia,Rhizopus, Wickerhamomyces, Issatchenkia, Saccharomyces, and Kazachstania. Model verification showed that the core microbiota significantly affected the composition of non-core microbiota (P < 0.01) and key flavor-producing enzymes (R > 0.8, P < 0.01), thus significantly affecting the flavor of base Baijiu. Simulated fermentation validated that the core microbiota can reproduce the fermentation process and quality of Xiaoqu light-aroma Baijiu. The succession of bacteria was mainly regulated by acidity and ethanol, while the fungi, especially non-Saccharomyces cerevisiae, were mainly regulated by the initial dominant bacteria (Acetobacter, Bacillus, and Weissella). This study will play an important role in the transformation of Xiaoqu light-aroma Baijiu fermentation from natural fermentation to controlled fermentation and the identification of core microbes in other fermented foods.

Effects of sorghum varieties on microbial communities and volatile compounds in the fermentation of light-flavor Baijiu.

Light-flavor Baijiu (LFB) fermentation is a representative spontaneous mixed-culture solid-state fermentation process in which sorghum is used as the raw material. Raw materials and microorganisms are crucial to the flavor formation and quality of LFB. However, the microbial and physicochemical dynamics of different sorghum varieties during LFB fermentation, as well as their impact on flavor compounds are still largely unknown. Herein, PacBio single-molecule real-time (SMRT) sequencing and headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC-MS) were applied to investigate microbial community succession and volatile flavor formation in glutinous/non-glutinous sorghum-based fermented grains during LFB fermentation. Fermented grains made of glutinous sorghum Liangnuo No. 1 (GLN) had higher bacterial α-diversity and lower fungal α-diversity than those with fermented grains prepared with non-glutinous red sorghum (NRS) (p < 0.05). The dominant microbial species were Saccharomyces cerevisiae, Acetobacter pasteurinus, and Lactobacillus helveticus, the latter two of which were the predominant bacteria observed at the end of fermentation in GLN and NRS, respectively. Moisture content and reducing sugar had a more significant impact on the microorganisms in GLN, while amino acid nitrogen, total free amino acids, and residual starch were the main driving factors driving the microbial community in NRS. The correlation network and discriminant analysis indicated that a relatively high content of 4-vinylguaiacol showed a significant positive association with significant differential microbial species in GLN. These results provided valuable insights for improving the quality of LFB.

Exploring the impact of initial moisture content on microbial community and flavor generation in Xiaoqu baijiu fermentation.

Moisture is essential in microbiota succession and flavor formation during baijiu fermentation. However, it remains unknown how moisture content affects microbiota, metabolism, and their relationship. Here, we compared the difference in volatiles, microbiota characteristics, and potential functions with different initial moisture contents (50 %, 55 %, 60 %, 65 %, 70 %). Results showed that the ratio of ethyl acetate to ethyl lactate and total volatile compounds content increased as the moisture content was elevated from 50 % to 70 %. As increasing moisture content, fermentation system microbiota dominated by Lactobacillus was formed more rapidly. Lactobacillus, Dekkera, and Pediococcus were positively correlated with moisture, promoting the production of propanol, acetic acid, butyric acid, and 2-butanol. The complexity and stability of ecological networks enhanced as moisture content increased (R2 = 0.94, P = 0.004). Our study revealed that moisture-drive microbiota was a critical contributor to flavor formation, providing the theoretical basis for moisture control to regulate flavor compounds.

Diet and high altitude strongly drive convergent adaptation of gut microbiota in wild macaques, humans, and dogs to high altitude environments.

Animal gut microbiota plays an indispensable role in host adaptation to different altitude environments. At present, little is known about the mechanism of animal gut microbiota in host adaptation to high altitude environments. Here, we selected wild macaques, humans, and dogs with different levels of kinship and intimate relationships in high altitude and low altitude environments, and analyzed the response of their gut microbiota to the host diet and altitude environments. Alpha diversity analysis found that at high altitude, the gut microbiota diversity of wild macaques with more complex diet in the wild environments is much higher than that of humans and dogs with simpler diet (p < 0.05), and beta diversity analysis found that the UniFrac distance between humans and dogs was significantly lower than between humans and macaques (p < 0.05), indicating that diet strongly drive the convergence of gut microbiota among species. Meanwhile, alpha diversity analysis found that among three subjects, the gut microbiota diversity of high altitude population is higher than that of low altitude population (ACE index in three species, Shannon index in dog and macaque and Simpson index in dog, p < 0.05), and beta diversity analysis found that the UniFrac distances among the three subjects in the high altitude environments were significantly lower than in the low altitude environments (p < 0.05). Additionally, core shared ASVs analysis found that among three subjects, the number of core microbiota in high altitude environments is higher than in low altitude environments, up to 5.34 times (1,105/207), and the proportion and relative abundance of the core bacteria types in each species were significantly higher in high altitude environments than in low altitude environments (p < 0.05). The results showed that high altitude environments played an important role in driving the convergence of gut microbiota among species. Furthermore, the neutral community model trial found that the gut microbiota of the three subjects was dispersed much more at high altitude than at low altitude, implying that the gut microbiota convergence of animals at high altitudes may be partly due to the microbial transmission between hosts mediated by human activities.