Two rearranged acylphloroglucinols with moderate neuroprotective effects from Hypericum ascyron Linn.

Phytochemical studies on the leaves and twigs of Hypericum ascyron Linn. led to the isolation of two previously undescribed rearranged polycyclic polyprenylated acylphloroglucinols (PPAP) with a 4,5-seco-3(2H)-furanone skeleton, named hyperascone A and B (1-2). Additionally, a known PPAP tomoeone A (3) and two known xanthones 1,3,5 -trihydroxy-6-O-prenylxanthone (4) and 3,7-dihydroxy-1,6-dimethoxyxanthone (5) were also isolated. The structures of the compounds were determined by the analysis of their spectroscopic data including HRMS, NMR and ECD. All of the five isolated compounds exhibited neuroprotective effects against MPP+ and microglia activation induced damage of SH-SY5Y cells.

Ectopic Spacer Acquisition in Streptococcus thermophilus CRISPR3 Array.

Streptococcus thermophilus relies heavily on two type II-A CRISPR-Cas systems, CRISPR1 and CRISPR3, to resist siphophage infections. One hallmark of these systems is the integration of a new spacer at the 5' end of the CRISPR arrays following phage infection. However, we have previously shown that ectopic acquisition of spacers can occur within the CRISPR1 array. Here, we present evidence of the acquisition of new spacers within the array of CRISPR3 of S. thermophilus. The analysis of randomly selected bacteriophage-insensitive mutants of the strain Uy01 obtained after phage infection, as well as the comparison with other S. thermophilus strains with similar CRISPR3 content, showed that a specific spacer within the array could be responsible for misguiding the adaptation complex. These results also indicate that while the vast majority of new spacers are added at the 5' end of the CRISPR array, ectopic spacer acquisition is a common feature of both CRISPR1 and CRISPR3 systems in S. thermophilus, and it can still provide phage resistance. Ectopic spacer acquisition also appears to have occurred naturally in some strains of Streptococcus pyogenes, suggesting that it is a general phenomenon, at least in type II-A systems.

Genome-wide analysis of fermentation and probiotic trait stability in Lactobacillus plantarum during continuous culture.

Trait stability of Lactobacillus plantarum was studied following daily subculture over a 90-d period. Acid and bile tolerance, self-aggregation ability, cell hydrophobicity, pathogen inhibition activity, and cholesterol removal ability of cultures subcultured 30 (Lp30), 60 (Lp60), or 90 (Lp90) times were not significantly different from the original strain (Lp0). However, carbohydrate metabolism patterns did change; the Lp0 culture was unable to use d-sorbitol, α-methyl-d-mannose, and d-raffinose, whereas Lp30, Lp60, and Lp90 cultures could. Furthermore, gluconate and gentiobiose were fully used by the Lp0 culture but only poorly used by the Lp30, Lp60, and Lp90 cultures. Milk fermentation test confirmed that L. plantarum was unable to use lactose throughout laboratory evolution. Six non-synonymous mutations in genome of the Lp30, Lp60, and Lp90 cultures were identified by whole-genome sequencing, including mutant gene encoding the phosphoglycerate mutase, which is closely related to the transport and metabolism of carbohydrates. These mutations may play an important role in changes of carbohydrate metabolism patterns observed. Understanding the evolutionary characteristics of L. plantarum will help in development for food industry.

Isoorientin attenuates benzo[a]pyrene-induced colonic injury and gut microbiota disorders in mice.

Benzo[a]pyrene (BaP, most toxic polycyclic aromatic hydrocarbon) is a global food-borne pollutant, and is associated with many diseases and gut microbiota disorders. The present study was designed to investigate the protective effects of isoorientin (ISO), a flavonoid compound in the human diet, on BaP-induced colonic damage and gut microbial disorders in mice. ISO was administered orally to mice at doses of 20 mg/kg body weight before BaP challenge (oral administration, 50 mg/kg body weight). The results revealed that ISO suppressed the BaP-induced reduction of body weight in mice, and it also prevented colonic damage, as evidenced by the increase in colon total superoxide dismutase (T-SOD) and glutathione peroxidase (GSH-Px) activities, and the decrease in colon malonaldehyde (MDA) and hydrogen peroxide (H2O2) levels, compared to BaP-treated mice. Meanwhile, we used 16S rRNA gene sequencing to investigate the impact of BaP with or without ISO on the colon contents associated bacteria in mice. ISO could relieve the BaP-induced change in the abundance of gut microbiota, especially the genera of Feacalibaculum, Lactobacillus, Acinetobacter, Desulfovibrio and Alistipes. And ISO ameliorated BaP-induced microbiota metabolic disturbance, especially the metabolic pathways of LPS and sulphur compounds. In conclusion, our findings indicated that ISO could be of significant advantage in suppressing the colonic injury and the gut microbiota disorder induced by BaP.

Low-Grade Nasopharyngeal Papillary Adenocarcinoma.

Low-grade nasopharyngeal papillary adenocarcinoma is a rare tumor, and only a limited number of cases are reported in the literature. The case reported in this study had long-term nasal catarrh with a runny nose and was admitted to the hospital. Computed tomography (CT) examination revealed polypoid mass in the nasopharynx. Pathological examination revealed typical papillary growth pattern of glandular epithelial cells. Immunohistochemical (IHC) staining showed the tumor cells to be diffusely positive for cytokeratin 7 (CK7), vimentin, and thyroid transcription factor 1 (TTF-1). The Ki-67 proliferation index was approximately 1%. In situ hybridization for latent Ebstein-virus (EBV) injection was negative. The patient did not exhibit recurrence or metastasis of the tumor.

Laboratory Evolution Assays and Whole-Genome Sequencing for the Development and Safety Evaluation of Lactobacillus plantarum With Stable Resistance to Gentamicin.

The goal of this work was to use laboratory evolution assays and whole-genome sequencing to develop and test the safety of a probiotic, Lactobacillus plantarum, with high-level of resistance to gentamicin. The evolution of L. plantarum was evaluated under the selective pressure from gentamicin and subsequently when the selective pressure was removed. After 30 days of selective pressure from gentamicin, the minimum inhibitory concentration (MIC) of L. plantarum to gentamicin increased from 4 to 512 µg/mL and remained stable at this level. After removing the selective pressure, the resistance of L. plantarum to gentamicin decreased to 64 µg/mL after 20 days, and remained stable thereafter. Although the MIC declined it was still higher than the cut-off value recommended by EFSA, indicating that the acquisition of gentamicin-resistance was an irreversible process. Using whole-genome sequencing, gene mutations were identified in the strains that had undergone selection pressure from gentamicin as well as in the strains where the selection pressure was subsequently removed. Specifically, four non-synonymous mutations were detected including one single nucleotide polymorphism (SNP), one insertion, and two structural variants (SVs), of which the mutations in genes encoding the drug resistance MFS transporter and transcriptional regulator of AraC family were only detected in the strains under selective pressure from gentamicin. The results indicate that these mutations play an important role in increasing the resistant levels of L. plantarum to gentamicin. The mobility analysis of mutant genes confirmed that they were not located on mobile elements of the genome of highly resistant L. plantarum, indicating that horizontal gene transfer was not possible.

Complete Genome Sequence of Escherichia coli Siphophage BRET.

The lytic Escherichia coli siphophage BRET was isolated from a chicken obtained at a local market in Abidjan, Côte d'Ivoire. Its linear genome sequence consists of 59,550 bp (43.4% GC content) and contains 88 predicted genes, including 4 involved in archaeosine biosynthesis. Phage BRET is related (95% nucleotide identity) to Enterobacteria phage JenK1.

Quality characteristics and antioxidant activities of goat milk yogurt with added jujube pulp.

This study aimed to evaluate the effects of the added jujube pulp on the quality characteristics and antioxidant activities of goat milk yogurt (GMY) during 28 days of refrigerated storage. Four GMY formulations were prepared, each varying in the added jujube pulp amount (Y0: not containing jujube pulp; YJ3, YJ6, YJ9: containing 3, 6, 9 g of jujube pulp per 100 g GMY, respectively). There was no significant differences in the viable counts, pH values and titratable acidities of all formulations during the storage. All formulations showed the viable counts all above 106 CFU/mL over the assessed storage period. However, YJ3 exhibited the desirable hardness, adhesiveness and water holding capacity. Moreover, the addition of jujube pulp weakened greatly the goaty flavor, improving the sensory acceptance, and increased the antioxidant activities of GMY. Therefore, GMY containing jujube pulp is optional for developing a novel goat dairy product with high added values.

Changes in the nutrients of camels' milk alter the functional features of the intestine microbiota.

Heat treatment alters the nutritive quality of camels' milk and thus the intestine microbiota, but the effect of heat treatment-induced nutrient loss on the functional features of the intestine microbiota is unknown. In this study, the influence of two heat treatments of camels' milk on the intestine microbiota was investigated to establish the correlations between milk nutrients and the functional features of the intestine microbiota. Camels' milk, heat treated at low (65 °C) or high (100 °C) temperatures, was administered to mice (LM = low; HM = high); control mice received sterile distilled water (CW = control). Intestine microbiota were compared in the three groups using metagenomic-based 16S rRNA gene high throughput sequencing. The results showed that the relative abundance of probiotic genera (Akkermansia, Bifidobacterium and Lactobacillus) was significantly higher in the LM group mice than in the HM group mice, due to the high-temperature degradation of the nutrients of camels' milk. The diversity of the intestine microbiota in mice receiving milk was lower than in the control group because of the intrinsically high antimicrobial components (lactoferrin and lysozyme) detected in camels' milk. Carbohydrate digestion/absorption, and cysteine and methionine metabolism were significantly higher in the intestine microbiota of the LM group mice than in the HM group mice owing to the corresponding degradation of lactose, cysteine and methionine in camels' milk at high temperatures. Changes in the nutrients of camels' milk affected the changes in the functional features of the intestine microbiota. This research suggests that low temperature heat treatment achieves nutrient preservation, but also encourages probiotic genera.

Bacterial Diversity in Chinese Rushan Cheese From Different Geographical Origins.

Rushan cheese, an essential part of the Bai culture, has been produced and consumed for centuries by the Bai people living mostly in Yunnan province of China, however, studies on the naturally occurring microbial communities of Rushan cheese are lacking. In this study, we applied high throughput sequencing technique to analyze the microbial compositions of Rushan cheese samples from three different geographical origins (i.e., Weishan, Eryuan, and Jianchuan). The microbiota in Weishan, Eryuan and Jianchuan Rushan cheese samples were distinct in terms of taxonomic composition and abundance. Linear discriminant analysis (LDA) of effect size (LEfSe) analysis found the characteristic taxonomic species in Weishan Rushan cheese samples were Lactobacillus pentosus, Lactobacillus crustorum, Lactobacillus brevis, Leuconostoc mesenteroides, and Pediococcus pentosaceus; the representing taxonomic species in Eryuan Rushan cheese samples were Lactobacillus kefiranofaciens, Lactococcus lactis, Acetobacter pasteurianus and Moraxella osloensis; by comparison, Acinetobacter was enriched in Jianchuan Rushan cheese samples. Characterization of the microbial diversity in Rushan cheese samples from different geographical origins will contribute to the understanding of microorganisms responsible for the Rushan cheese fermentation, and enable us to develop bioresources derived from Rushan cheese in the future.

Effects of Natural Flavonoid Isoorientin on Growth Performance and Gut Microbiota of Mice.

Isoorientin (ISO) is a natural flavonoid, which is a 6- C-glucoside of luteolin, and has been demonstrated to possess multiple biological properties. In this study, the effects of ISO on the growth performance and gut microbiota of BALB/c mice were investigated. The results showed that ISO could promote food intake and body weight gain, increase the digestibility of crude proteins and utilization of the gross energy, and strengthen antioxidant capacity of mice. We also demonstrated it has no side effects on hepatic and renal functions. Moreover, ISO inhibited the growth of most bacteria in gut microbiota, especially the pathogenic genera of Alistipes, Helicobacter, and Oscillibacter, which could lead to inflammation. Metabolisms of epithelial cell signaling in Helicobacter pylori infection, lipopolysaccharide (LPS) biosynthesis, and LPS biosynthesis proteins in gut microbiota of the control group were more abundant than those in the ISO group, while lipid metabolism and vitamin B6 metabolism were enriched in the ISO group. We found the changes in enrichments of metabolic pathways of the gut microbiota along with the ISO application were positively correlated with the antioxidation, anti-inflammation, and antibiosis. This work provided a fundamental basis for the future development of ISO-functional foods used for resistance to oxidation, inflammation, and pathogens.

Consumption of Goats' Milk Protects Mice From Carbon Tetrachloride-Induced Acute Hepatic Injury and Improves the Associated Gut Microbiota Imbalance.

Drugs used to treat liver diseases have serious side effects; it is important to search for safe functional foods with hepatoprotective functions and few side effects. In this study, potential hepatoprotective effects of goats' milk and cows' milk on mice with CCl4-induced acute hepatic injury were evaluated. We also elucidated the role of goats' and cows' milk on the regulation of CCl4-induced gut microbiota imbalance. In mice with liver damage induced by CCl4, administration of goats' milk for 7 days prior to injection of CCl4 had beneficial effects on the indicators of liver damage within 1 day: the area of liver necrosis was small; activity of alanine transaminase (ALT) and aspartate transaminase (AST) and expression of the genes CYP2E1 and TNF-α were lower than that of model group of mice. By 7 days after CCl4 injection, there were no significant differences in liver damage indicators (ALT, AST, malondialdehyde, superoxide dismutase, and glutathione) between the goats' milk group, which continued to receive goats' milk, and the untreated control group of mice showing that goats' milk continued to protect against liver damage. Throughout the entire experiment, the community of gut microbes from mice in the goats' milk treatment was more similar to the untreated control group than to the cows' milk group and the model group, indicating that intake of goats' milk prior and post-CCl4 injection effectively prevented and alleviated the intestinal microbial disorder that caused by CCl4 in mice. Our research suggests that goats' milk could be developed as a potential functional food to prevent/protect against liver injury.

Influence of Bactrian camel milk on the gut microbiota.

Bactrian camel milk has become popular in the market as an important source of nutrients with diverse functional effects. In this study, the influence of Bactrian camel milk on the gut microbiota of mice was studied using metagenomic-based sequencing of the V3 and V4 hypervariable regions of the 16S rRNA gene. Bioinformatics analysis showed that Firmicutes and Bacteroidetes were the predominant phyla, accounting for more than 80% of the bacteria present. At the genus level, Allobaculum, Akkermansia, Romboutsia, Bifidobacterium, and Lactobacillus were most abundant in the gut microbiota; of these, Allobaculum and Akkermansia were the predominant genera, representing 40.42 and 7.85% of all the bacteria present, respectively. Camel milk was found to reduce relative abundance of Romboutsia, Lactobacillus, Turicibacter, and Desulfovibrio (decreased by 50.88, 34.78, 26.67, and 54.55%, respectively) in the gut microbiota compared with the control. However, some genera such as Allobaculum, Akkermansia, and Bifidobacterium in the gastrointestinal flora increased in abundance in the presence of camel milk; these genera are correlated with beneficial effects for organisms. Our research suggests that the gut microbiota should be taken into account when conducting functional studies on camel milk, and this work provides a useful foundation for further study on functions of camel milk.

Unique Microbial Diversity and Metabolic Pathway Features of Fermented Vegetables From Hainan, China.

Fermented vegetables are typically traditional foods made of fresh vegetables and their juices, which are fermented by beneficial microorganisms. Herein, we applied high-throughput sequencing and culture-dependent technology to describe the diversities of microbiota and identify core microbiota in fermented vegetables from different areas of Hainan Province, and abundant metabolic pathways in the fermented vegetables were simultaneously predicted. At the genus level, Lactobacillus bacteria were the most abundant. Lactobacillus plantarum was the most abundant species, followed by Lactobacillus fermentum, Lactobacillus pentosaceus, and Weissella cibaria. These species were present in each sample with average absolute content values greater than 1% and were thus defined as core microbiota. Analysis results based on the alpha and beta diversities of the microbial communities showed that the microbial profiles of the fermented vegetables differed significantly based on the regions and raw materials used, and the species of the vegetables had a greater effect on the microbial community structure than the region from where they were harvested. Regarding microbial functional metabolism, we observed an enrichment of metabolic pathways, including membrane transport, replication and repair and translation, which implied that the microbial metabolism in the fermented vegetables tended to be vigorous. In addition, Lactobacillus plantarum and Lactobacillus fermentum were calculated to be major metabolic pathway contributors. Finally, we constructed a network to better explain correlations among the core microbiota and metabolic pathways. This study facilitates an understanding of the differences in microbial profiles and fermentation pathways involved in the production of fermented vegetables, establishes a basis for optimally selecting microorganisms to manufacture high-quality fermented vegetable products, and lays the foundation for better utilizing tropical microbial resources.

Evaluation of the nutrition and function of cow and goat milk based on intestinal microbiota by metagenomic analysis.

Milk contains nutrients needed by the body, and the main components of different animal milk vary. Accordingly, we evaluated cow and goat milk's nutrition and their effects on the gut microbiota in mice models using a high-throughput 16S rRNA sequencing technology. The intestinal microbiota of mice changed significantly after the intake of cow and goat milk, and the goat milk had a greater effect on the intestinal microbial community than the cow milk. Bifidobacterium, Allobaculum, Olsenella and Akkermansia grew significantly in both cow and goat milk groups compared with the control group, indicating that milk positively affected their growth. We also found that the citrate cycle (TCA cycle), pyruvate metabolism, and amino sugar and nucleotide sugar metabolism, as well as lipoic acid metabolism, were higher in the goat milk group than in the cow milk group. Association analysis of milk components and their representative intestinal microbiota showed that casein, αs1-casein, and ß + κ-casein were positively correlated with Enterococcus and Allobaculum, and negatively correlated with Roseburia. Protein and αs2-casein were positively associated with Akkermansia, Bifidobacterium and Eubacterium.

Whole-genome sequencing reveals the mechanisms for evolution of streptomycin resistance in Lactobacillus plantarum.

In this research, we investigated the evolution of streptomycin resistance in Lactobacillus plantarum ATCC14917, which was passaged in medium containing a gradually increasing concentration of streptomycin. After 25 d, the minimum inhibitory concentration (MIC) of L. plantarum ATCC14917 had reached 131,072 µg/mL, which was 8,192-fold higher than the MIC of the original parent isolate. The highly resistant L. plantarum ATCC14917 isolate was then passaged in antibiotic-free medium to determine the stability of resistance. The MIC value of the L. plantarum ATCC14917 isolate decreased to 2,048 µg/mL after 35 d but remained constant thereafter, indicating that resistance was irreversible even in the absence of selection pressure. Whole-genome sequencing of parent isolates, control isolates, and isolates following passage was used to study the resistance mechanism of L. plantarum ATCC14917 to streptomycin and adaptation in the presence and absence of selection pressure. Five mutated genes (single nucleotide polymorphisms and structural variants) were verified in highly resistant L. plantarum ATCC14917 isolates, which were related to ribosomal protein S12, LPXTG-motif cell wall anchor domain protein, LrgA family protein, Ser/Thr phosphatase family protein, and a hypothetical protein that may correlate with resistance to streptomycin. After passage in streptomycin-free medium, only the mutant gene encoding ribosomal protein S12 remained; the other 4 mutant genes had reverted to the wild type as found in the parent isolate. Although the MIC value of L. plantarum ATCC14917 was reduced in the absence of selection pressure, it remained 128-fold higher than the MIC value of the parent isolate, indicating that ribosomal protein S12 may play an important role in streptomycin resistance. Using the mobile elements database, we demonstrated that streptomycin resistance-related genes in L. plantarum ATCC14917 were not located on mobile elements. This research offers a way of combining laboratory evolution techniques and whole-genome sequencing for evaluating antibiotic resistance in probiotics.

Effects of microbial diversity on nitrite concentration in pao cai, a naturally fermented cabbage product from China.

Pao cai is a spontaneously fermented cabbage where native bacteria may have an important influence on nitrite content during fermentation. In this research, we used metagenomic-based 16S rRNA gene amplicon sequencing to analyze differences in bacterial composition of pao cai from Hohhot City (northern China) and Guiyang City (southern China). Alongside this, metagenome functional features from the 16S rRNA genes of the microbiome were predicted and correlated with the nitrite content of pao cai. Nitrite-reducing bacterial genera were identified including Lactobacillus (73.37%), Pediococcus (0.93%), Acinetobacter (0.74%), Leuconostoc (0.31%), Weissella (0.14%), Streptococcus (0.09%), Megamonas (0.08%), Enterococcus (0.07%), and Alistipes (0.06%). Lactobacillus was the predominant genus in both the northern and the southern pao cai samples and was significantly negatively correlated with nitrite content; it was more abundant in southern samples than northern samples. Based on determination of alpha and beta diversities of the microbiome in samples, differences in the microbiome of northern and southern pao cai were demonstrated that may influence nitrogen metabolism. This research suggests that 16S rRNA gene amplicon sequencing is an effective way to comprehensively study the microbes with potential nitrite formation or decomposition ability instead of investigating the individual bacterial genera.

Lactobacillus plantarum HNU082-derived improvements in the intestinal microbiome prevent the development of hyperlipidaemia.

Restricted by research techniques, the probiotic-derived changes in the microbiome and microbial metabolites correlated with the potential prevention of hyperlipidaemia have remained undiscovered. In the present research, a metagenomic approach was applied to describe Lactobacillus plantarum HNU082 consumption-derived changes in the intestinal microbiome and their correlation with the occurrence and development of hyperlipidaemia. Principal coordinate analysis based on UniFrac distances indicated that the intestinal microbiota was profoundly altered in the hyperlipidaemia group, and probiotic consumption regulated the bias in the intestinal microbial structure in hyperlipidaemia. Bifidobacterium, Lactobacillus, Akkermansia and Faecalibacterium were significantly increased in the probiotic group, and the genera Clostridium, Natranaerovirga and Odoribacter were significantly increased in the hyperlipidaemia group. Further analysis based on metabolic pathways revealed that pyruvate metabolism, glycerolipid metabolism, propanoate metabolism, and fatty acid biosynthesis were enriched in the probiotic and control groups. In contrast, the pathways of secondary bile acid and lipopolysaccharide biosynthesis were enriched in the hyperlipidaemia group. Finally, we constructed a network to better explain the potential mechanism of hyperlipidaemia prevention. The present basic research will promote our understanding of the probiotic action mechanism in hyperlipidaemia therapy and provide new insight into the design and application of probiotic-containing functional foods.

Differential enumeration of subpopulations in concentrated frozen and lyophilized cultures of Lactobacillus delbrueckii ssp. bulgaricus.

Differential enumeration of subpopulations in concentrated frozen and lyophilized cultures of Lactobacillus delbrueckii ssp. bulgaricus ND02 derived from 2 propagation procedures was determined. The subpopulations consisted of 3 categories (physiological states): viable cells capable of forming colonies on agar plates (VC+), viable cells incapable of forming colonies on agar plates (VC-), widely referred to as viable but nonculturable (VBNC) cells, and nonviable or dead cells (NVC). Counts of VC+ were recorded using a conventional plate count procedure. A fluorescent vital staining procedure that discriminates between viable (VC+ and VC-) and NVC cells was used to determine the number of viable and nonviable cells. Both propagation procedures had 2 variables: in procedure (P)1, the propagation medium was rich in yeast extract (4.0%) and the pH was maintained at 5.7; in P2, the medium was devoid of yeast extract and the pH was maintained at 5.1. The results showed that post-propagation operations-concentration of cells by centrifugation and subsequent freezing or lyophilization of cell concentrate-induced different degrees of transience from VC+ to VC- states in cells derived from P1 and P2. Compared with cells derived from P2, cells from P1 were more labile to stress associated with centrifugation, freezing, and lyophilization, as revealed by differential counting.

Bacterial diversity in goat milk from the Guanzhong area of China.

In this study, the V3 and V4 regions of the 16S rRNA gene from metagenomic DNA were sequenced to identify differences in microbial diversity in raw milk of Saanen and Guanzhong goats from the Guanzhong area of China. The results showed that Proteobacteria was the predominant phylum, accounting for 71.31% of all phyla identified in milk from the 2 breeds, and Enterobacter was the predominant genus (24.69%) within the microbial community. Microbial alpha diversity from Saanen goat milk was significantly higher than that of Guanzhong goat milk based on bioinformatic analysis of indices of Chao1, Shannon, Simpson, observed species, and the abundance-based coverage estimator. Functional genes and their likely metabolic pathways were predicted, which demonstrated that the functional genes present in the bacteria in goat milk were enriched in pathways for amino acid metabolism and carbohydrate metabolism, which represented 11.93 and 11.23% of functional genes, respectively. Physicochemical properties such as pH, protein, fat, and AA levels were also determined and correlations made with microbial diversity. We detected a significant difference in the content of lactose and 6 AA, which were higher in Saanen milk than in Guanzhong milk, and positively correlated with microbial carbohydrate metabolism and AA metabolism. Lactococcus, Lactobacillus, Bifidobacterium, Enterococcus, and Streptococcus, which are lactose-utilizing genera, were more abundant in Saanen milk than in Guanzhong milk. Higher levels of lactose in Saanen goat milk may explain its greater microbial diversity. We also demonstrated that most of the AA metabolism-related bacterial genera (e.g., Massilia, Bacteroides, Lysobacter) were enriched in Saanen goat milk. In this research, both probiotic and pathogenic bacteria were identified in goat milk, which provided the microbial information necessary to direct the utilization of beneficial microbial resources and prevent the development of harmful organisms in goat milk.