In this study, 12 strains of Akkermansia muciniphila were isolated and characterized from healthy volunteers from different regions of Xinjiang Uygur Autonomous Region, China. Through whole-genome phylogenetic analysis, the genetic differences among these strains were compared. Their genome sizes ranged from 2.64 to 2.98 Mb, with GC contents between 55.1% and 55.7%. According to the phylogenetic tree constructed based on average nucleotide identity (ANI) and core genes, we categorized all isolates into three distinct subgroups. The results indicated that subgroup Ⅱ exhibited the highest acid and bile salt tolerance, with aggregation rates > 60% after 48 h and hydrophobicity of (32.00 ± 0.02)% after 15 min. This subgroup also had superior radical scavenging capacity against 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2’-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) cation radical. Hemolysis assays showed no significant hemolytic rings, indicating that all strains were safe for short-term usage. All strains were resistant to aminoglycoside antibiotics (streptomycin and gentamicin) and susceptible to glycopeptide antibiotics (vancomycin). The antibiotic resistance phenotype results were not completely consistent with the gene detection results. Genomic sequencing identified the glycoside hydrolase families 2 (GH2) and 20 (GH20). Carbon source utilization analyses indicated that galactooligosaccharides, soybean oligosaccharides, and xylitol synergistically promoted the proliferation of A. muciniphila. Taken together, subgroup Ⅱ strains exhibit great potential for use as probiotics.

In this study, 23 strains of Bifidobacterium longum subsp. infantis were isolated and identified from 150 infant fecal samples in Northwest China by a culture method combined with polymerase chain reaction, with an isolation rate of only 10.67%. The genomes and probiotic properties of these strains of B. infantis were compared and analyzed. Genomic analysis showed that the average GC content, genome size, and number of coding sequences of B. infantis were 59.81%, 2.61 Mb, and 2273, respectively. Phylogenetic analysis based on core genes and average nucleotide identity (ANI) analysis showed that strains from the same geographical origin had high genetic similarity and close phylogenic relationships. There were differences in gene families related to plant-derived carbohydrate metabolism among strains. Carbohydrate metabolism experiments showed that most B. infantis strains were able to metabolize prebiotics such as galactooligosaccharides, oligofructose, and inulin, corroborating the presence of the glycoside hydrolase (GH) 32 and GH43 gene families, and four strains (A47X1, A79X4, A79X3, and S19X4) were able to utilize xylose. B. infantis S8X8 and S5X8_2 most effectively inhibited diarrheagenic Escherichia coli CICC-10411, enterotoxigenic E. coli CICC-10421, Salmonella enterica subsp. enterica serovar Typhimurium CICC-10420, enterohaemorrhagic E. coli CICC-21530, S. enterica subsp. enterica serovar Enteritidi CGMCC1.10754-SM1, but did not inhibit Listeria monocytogenes CGMCC1.9136-LS1. Intrinsic resistance genes to antibiotics such as rifampicin, mupirocin, and aminoglycoside, but not pathogenic virulence factors, were detected in the genome of B. infantis. All B. infantis strains were susceptible to vancomycin, gentamicin and streptomycin. This study provides a reference for the development of personalized probiotic preparations for infants in different regions.

Co-culturing fermentation can improve the bioactivity and metabolic diversity of bacterial strains. In this study, we explored the cooperation between Bifidobacterium animalis subsp. lactis HN-3 (B.an3) and Lacticaseibacillus paracasei YL-29 (L.cp29) by non-targeted metabolomics and prokaryotic transcriptomics analysis. B.an3 and L.cp29 co-culture showed greater growth than the monoculture fermentation through 7 growth regulating metabolic pathways that facilitated the accumulation of monoculture growth-correlated markers, including, raffinose, stachyose, and  L-thymidine involved in nucleotide and galactose metabolism. On the other hand, compared to the monoculture fermentation, the significantly enhanced functional activities of the co-culture were associated with 74 and 68 significantly altered metabolites, such as phenylacetaldehyde, succinic acid, and trans-cinnamic acid with antioxidant, anti - inflammatory, and anti-bacterial properties. Overall, this study revealed the cooperative beneficial relationship between B.an3 and L.cp29. It offered novel insights into the co-culture mechanisms, providing a basis for further development of microbial natural products.

In this study, the population structure and evolutionary relationships of 59 Enterococcus faecalis strains isolated from breast milk, cheese, camel milk, mare milk and cold water fish from Xinjiang were analyzed by multilocus sequence typing (MLST). All the isolates were allocated into 12 sequence types, including three clonal complexes and three singletons. None of the sequence types were found to belong to high risk clonal complexes. Housekeeping gene split decomposition analysis indicated that gene recombination could be a major driving force in the evolution of E. faecalis. The results of minimum spanning tree indicated these E. faecalis strains were relatively weakly related to their geographical origin. Although eBURST and phylogenetic analysis demonstrated that the isolates from breast milk and cold water fish exhibited host specificity, E. faecalis clones closely related to them were still detected in breast milk, cheese, mare milk and camel milk. Taken together, E. faecalis from different hosts can adapt to new niches and spread via production practice and the food chain. Continuous monitoring is necessary to reduce the potential risk of zoonotic diseases

Thirty-eight strains suspected of being lactic acid bacteria were isolated from 15 donkey milk samples collected in Hami, Xinjiang, of which seven strains were found to have obvious milk coagulation characteristics. The strains were identified by 16S rRNA gene sequencing as Pediococcus acidilactici HL12-21, Pediococcus pentosaceus HL29-5, Enterococcus mundtii HL30-3, Lactobacillus plantarum HL21-44, Lactobacillus coryniformis HL26-24, Lactobacillus curvatus HL29-1 and Leuconostoc lactis HL13-23. They were screened for their milk coagulation time, acid-producing capacity, post-acidification capacity, aroma-producing capacity, sensory characteristics and viable counts during cold storage, of which HL12-21, HL29-5, HL21-44 and HL29-1 possessed better acid-producing and aroma-producing capacity and weaker post-acidification capacity, and the single culture fermented milk had the highest comprehensive scores for color, texture and flavor. The number of viable bacteria still remained above 10⁶ CFU/mL after storage at 4 ℃ for 20 days. In addition, the tolerance of the seven strains and the probiotic bacterium Lactobacillus rhamnosus GG to simulated gastrointestinal fluid, as well as their antimicrobial spectra, antibiotic resistances and antioxidant activities were compared. The results showed that HL29-5 and HL30-3 were superior to the other strains in terms of all above probiotic properties, with special reference to the highest scavenging rates against hydroxyl, 1,1-diphenyl-2-picrylhydrazyl (DPPH) and superoxide anion free radicals (over 30%). Based on our results, Pediococcus pentosaceus HL29-5 holds great potential as a probiotic starter culture for developing specialty yogurt.

In this study, a combination of an improved mucin enriched medium with real-time polymerase chain reaction (real-time PCR) was used to test 48 samples of maternal and infant feces for Akkermansia muciniphila (Akk). Under optimized conditions, 24 Akk strains were isolated from eight positive samples. All these strains were confirmed as Akk by 16S rRNA gene sequencing and PCR with Akk-specific primers. Repetitive extragenic palindrome-polymerase chain reaction (rep-PCR) fingerprinting classified the 24 strains into four genotypic groups. Subsequently, these strains were tested in vitro for simulated gastrointestinal fluid tolerance, hydrophobicity, antibiotic susceptibility, and glycan utilization capacity. The results showed that strains HN18D-1, HN18D-3, and WW48D1-13 had the highest tolerance to simulated gastric and intestinal fluids. All Akk strains were resistant to vancomycin, clindamycin, kanamycin and erythromycin. Xylooligosaccharides and soybean oligosaccharides had prebiotic effects on the Akk strains. Collectively, Akk isolates HN18D-1, HN18D-3 and WW48D1-13 can be used as potential probiotic candidates for subsequent in-depth studies.

This study was conducted to isolate and identify Bifidobacterium from the feces of Kazakh school-age children in Yining, Xinjiang and evaluate the in vitro probiotic characteristics of B. longum subsp. longum isolates. By groEL gene sequencing and repetitive element sequence-based polymerase chain reaction (rep-PCR) fingerprinting, 416 Bifidobacterium strains were identified to belong to B. longum, B. bifidum, B. pseudocatenulatum, B. catenulatum and B. breve. According to the fingerprints of B. longum subsp. longum, 27 genotypes showed genetic differences between individual strains and the coexistence of multiple strains in the gut was found. The in vitro experimental results showed that out of 27 representative strains, strains 2B3-21, 1B23-11, 2B33-3, and 1B68-16 were optimal in acid and bile salt tolerance, strains 1B68-16, 2B13-5, 2B33-3, and 1B39-2 had broad-spectrum antibacterial properties, and strains 1B38-1, 2B33-3, 1B68-16, and 2B13-28 showed a strong antioxidant capacity. Considering the antibiotic resistance of all strains and their ability to utilize plant-derived glycans, strains 1B38-1 and 2B13-28 were selected to assess their in vivo probiotic potentials. This study may lay the foundation for the development of excellent probiotics and related products for populations from specific areas.

This study was focused on 16 strains of Ligilactobacillus ruminis isolated from fecal samples of healthy persons from different families in Kashi, Xinjiang. Genomic and phylogenetic analysis were conducted, and the in vitro probiotic characteristics of the strains were compared. Genomic analysis revealed that the average genome size, gene number, and GC content of the L. ruminis strains were 1.4 Mb, 1374, and 43.55%, respectively. Notably, there were significant differences in the number of strain-specific genes, ranging from 3 to 886 (strain K646-58L had a notably higher number of specific genes compared with all other strains). In phylogenetic analysis, strains from the same family did not cluster together as closely based on their hosts’ genetic relatedness. The carbon source utilization experiments showed that the L. ruminis strains could utilize soybean oligosaccharides, cottonseed xylose, and maltodextrin, but not sorbitol or xylitol. The carbohydrate-active enzyme database (CAZy) annotated a large number of genes involved in polysaccharide substrate metabolism, such as the glycoside hydrolase (GH)1 and GH13 gene families. The 16 strains showed resistance to aminoglycosides but susceptibility to tetracyclines and chloramphenicol, which was not completely consistent with resistance gene prediction. All L. ruminis strains had high self-aggregation ability (> 50%) and good hydrophobicity (> 20%). Based on the genetic and phenotypic characteristics, L. ruminis had excellent probiotic properties, especially strains K227-6L and K645-5L. This study lays the theoretical foundation for the development and application of potential probiotic strains.

Probiotics have been proven to play a positive role in the prevention and treatment of diabetes. The gut microbiota of different populations harbors an extremely rich diversity of species and strains. This study aimed to explore potential new probiotic resources from the intestine of Tajik children with the goal of discovering new strains that can be used for the prevention and treatment of diabetes. In this study, Bifidobacterium strains were isolated from the intestine of healthy Tajik children in Xinjiang and identified using groEL gene sequencing. These strains were then screened for their in vitro probiotic characteristics to identify potential anti-diabetic strains. The results showed that 1579 Bifidobacterium strains were isolated and purified from the intestine of 62 children, with Bifidobacterium longum subsp. longum being the dominant ones (591 isolates). A total of 76 sequenced strains of B. longum subsp. longum from 33 samples containing B. longum, at least one strain of which was from each sample, were analyzed for in vitro probiotic characteristics. The results showed that five B. longum subsp. longum strains (TXX165-6, TXX127-13, TXX13-17, TXX51-1, and TXY63-27) exhibited a survival rate exceeding 60% in simulated gastrointestinal fluid and demonstrated good carbon source utilization capabilities. All of their cell-free supernatants exhibited strong antioxidant activity and α-glucosidase inhibitory activity, scavenging over 82% of 2,2’-azino-bis-(3-ethylbenzthiazoline-6-sulphonic acid) (ABTS) cation radical and over 68% of 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical. Strain TXX165-6 exhibited the highest surface hydrophobicity (78.46%) and surface self-aggregation ability (49.15%). Strain TXX51-1 displayed the second-highest surface hydrophobicity (67.30%) and inhibited 68.75% of α-glucosidase activity, which was significantly superior to the model probiotic Lacticaseibacillus rhamnosus GG (20.15%). Therefore, strains TXX165-6 and TXX51-1 are promising candidates for further animal experiments to assess their potential as potential anti-diabetic strains.