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.

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.

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.

Antibiotic resistance genes, as newly emerging contaminants, have become a serious challenge to public health through the food chain. The gut of humans and animals is an important reservoir for the development and dissemination of antibiotic resistance genes because of the great abundance and diversity of intestinal micro biota. In the present study, we evaluated the influence of goat milk on the diversity and abundance of antibiotic resistance genes and gut microbial communities, especially pathogenic bacteria. Male mice were used, 12 for each of the 2 groups: a control group that received sterile distilled water and a treated group that received goat milk, and gut microbiota and antibiotic resistance genes were compared in these groups using metagenomic analysis. The results revealed that ingestion of goat milk decreased the diversity and abundance of antibiotic resistance genes in the mice gut. The relative abundance of fluoroquinolone, peptide, macrolide, and beta-lactam resistance genes in the total microbial genes significantly decreased after the intervention. Goat milk intake also significantly reduced the abundance of pathogenic bacteria, such as Clostridium bolteae, Clostridium symbiosum, Helicobacter cinaedi, and Helicobacter bilis. Therefore, goat milk intake might decrease the transfer potential of antibiotic resistance gene to pathogenic bacteria in the gut. In addition, bacteria with multiple resistance mechanisms accounted for approximately 4.5% of total microbial communities in the control group, whereas it was not detectable in the goat milk group, indicating the total inhibition by goat milk intake. This study highlights the influence of goat milk on antibiotic resistome and microbial communities in the gut, and provides a new insight into the function of goat milk for further study.