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Staphylococcus aureus is one of the main pathogens causing mastitis in dairy animals worldwide. It is an important opportunistic pathogen of raw milk, and the enterotoxin causes significant food poisoning. Monitoring the antibiotic resistance of S. aureus in raw milk is helpful for a risk assessment of S. aureus. In this study, 62 strains (43.1%) of S. aureus were isolated from 144 retail raw milk samples of different varieties from four regions in northern Xinjiang, China. Among them, the isolation rates at Shihezi, Hami, Altay, and Tacheng were 58.1% (54/93), 12.9% (4/31), 18.2% (2/11), and 22.2% (2/9), respectively. The isolation rate of positive strains in cow milk samples was the highest (61.7%, 37/60), followed by camel milk (35.9%, 23/64), and horse milk (10.0%, 2/20). The results of the classical virulence genes test showed that 12.9% (8/62) of the isolates carried at least one virulence gene. The main genotype was see (6.5%, 4/62), followed by sea+sec (3.2%, 2/62), sea (1.6%, 1/62), and sec (1.6%, 1/62). The analysis of 13 resistance genes and the susceptibility to 12 different antibiotics of 62 isolates showed that 80.6% (50/62) of the strains were resistant to at least one antibiotic, and 46.8% (29/62) were resistant to three or more antibiotics. The isolated strains had the highest resistance rate to penicillin (72.6%, 45/62), and 25.8% (16/62) of the isolates carried the blaZ resistance gene. In addition, 32 strains (51.6%, 32/62) of methicillin-resistant S. aureus were detected. All isolates had the ability to form biofilms. The pulsed-field gel electrophoresis results showed that the 47 isolates revealed 13 major pulsotypes (P1–P13) and 26 subtypes with 80% similarity, indicating the overall genetic diversity in the distribution area and sources of the samples. These findings indicate that S. aureus causes serious pollution of raw milk in northern Xinjiang, which has a negative effect on public health. Therefore, control measures and continuous monitoring should be undertaken to ensure the quality and safety of raw milk.

The maternal gut is the principal source of commensal bacteria in the infant gut during the lactation stage, where breast milk acts as an intermediary for the transfer of potential probiotic bacteria consortia, including Lactobacillus. This study aimed to characterize the bacterial communities in human milk, maternal, and infant feces in a small yet very homogeneous cohort of 25 healthy mother–infant pairs in northwestern China (n = 25, infant age from 7 days to 2 years), with special emphasis on the cooccurrence and vertical transfer of Lactobacillus phylotypes at the species or strain level in mother-breast milk-infant triads. Accurate sequencing analysis revealed that among 73 Lactobacillus zero-radius operational classification units (ZOTUs) identified, 58 belonging to 18 recognized species or species groups were distributed in all three types of samples. Lactobacillus ruminis, L. mucosae and L. gasseri-johnsonii as true residents were the most represented in all three ecosystems, whereas the content of Lactobacillus phylotypes commonly developed as probiotics was not dominant. While the numbers of Lactobacillus species in breast milk and infant feces were greater than that in maternal feces, principal coordinates analysis (PCoA) based on beta diversity, coupled with the frequency of isolates determined by culture methods, showed that the Lactobacillus community in the infant gut was more similar to that in the maternal gut than to that in breast milk, suggesting that the gut is niche selective for Lactobacillus populations. In addition, identical strains of L. ruminis, L. paracasei, L. mucosae and L. salivarius were isolated from multiple mother–infant pairs, supporting the hypothesis that vertical transfer of bacteria via breastfeeding contributes to the initial establishment of the microbiota in the developing infant intestine.

Breast milk acts as an intermediary for the transfer of functionally important commensal bacteria from mother to infant, especially for Bifidobacterium that can colonize the infant gut. However, the vast majority of rRNA amplicon-based studies reported the conspicuous intercohort and interindividual variation for the prevalence of Bifidobacterium in breast milk. In order to elucidate whether Bifidobacterium phylotypes persistently co-occured at the species or strain level in mother–breast milk–infant triads, we analyzed collectively the next-generation sequencing (NGS) datasets of bacterial 16S rRNA gene and the Bifidobacterium-specific groEL gene from maternal feces, breast milk, and infant feces in a small yet very homogeneous cohort of 25 healthy Uyghur mother–infant pairs (lactation for 7–720 days) in Kashgar, Xinjiang, China. Overall, 16S rRNA gene analysis showed that microbiome in the newborn gut was closer to that of breast milk in the first 4 months of lactation, and subsequently showed an obvious trend of adulthood at 6–12 months. Based on the BLAST accurate taxonomic result of the representative sequences of all ASVs (amplicon sequencing variants), only three sets of ASVs could be clearly assigned into Bifidobacterium species, whereas the remaining eight sets of ASVs corresponded to four indefinite Bifidobacterium species group. By contrast, the groEL gene dataset was partitioned into 376 ASVs, at least belonging to 13 well-known Bifidobacterium species or subspecies, of which 15 ASVs, annotated to seven well-known Bifidobacterium species or subspecies, showed triadic synchronism in most 23 mother–infant pairs tested. However, several other rare bifidobacterial phylotypes, which were frequently encountered in animals, were found to display no correspondence of the presence between the three ecosystems of mother–infant pairs. Our test results were obviously to support the hypothesis that breast milk acts as an intermediary for the transfer of probiotic commensal bacteria from mother to infant, especially for endosymbiotic Bifidobacterium that can colonize the infant gut. Some oxygen-insensitive exogenous Bifidobacterium phylotypes with a cosmopolitan lifestyle may be indirectly transferred to breast milk and the infant’s intestinal tract through environmental contamination. Thus, the groEL gene proved to be a very effective target for the depth resolution of Bifidobacterium community by high-throughput sequencing technologies.

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