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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.

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.

Background/Aim. Staphylococcus aureus (S. aureus) is a gram-positive pathogen that causes various human diseases. S. aureus causes pneumonia, which is characterized by localized tissue necrosis. The aim of the study was to explore the expression of mouse β-defensin 3 (mBD-3) induced by S. aureus in mouse lungs and the effect of mBD-3 expression on the mitogen-activated protein kinase (MAPK) pathway. Methods. An experimental model of S. aureus pneumonia in mice was developed, and the expression of mBD-3 and activation of the MAPK pathway were investigated using the methods of immunofluorescence and western blot. Results. The experimental model was created successfully. The number of white blood cells was elevated 48 and 72 hrs after the introduction of bacteria through mouse airways, and bronchiolar mucosal hyperemia was observed, along with a large number of white blood cells and mucus in the bronchioles. The mBD-3 expression levels 48 and 72 hrs after the induction of infection were greater than the levels in the control group and 24 hrs after the induction. The amount of phosphorylated extracellular signal-regulated kinase (ERK1/2) was increased 48 and 72 hrs after infection induction, compared with the levels in the control group and 24 hrs after induction. The expression of mBD-3 was lower when ERK1/2 phosphorylation was inhibited by the U0126 inhibitor. Conclusion. S. aureus in experimental pneumonia mouse model accelerates mBD-3 expression in the mouse lung mainly through an ERK1/2-dependent signaling pathway.

Owing to its high nutritional content, raw milk contains a rich microbiota. Thus, to study microorganisms present in raw milk available in Xinjiang China, 142 raw milk samples from seven animal breeds (cow, sheep, goat, donkey, horse, camel, and yak) and four regions (Hami, Tarbagatay, Kashgar, and Ili) were analyzed by high-throughput DNA sequencing. These microorganisms were characterized by 10 dominant phyla. Proteobacteria (68.33%) was the major phylum, followed by Firmicutes (18.80%) and Thermi (3.16%). Horse milk contained more Bacteroidetes, sheep milk contained more Gammaproteobacteria, and donkey milk contained more unclassified sequences. Camel and donkey milk contained the highest and lowest bacterial diversity compared with that contained by the remaining milk samples, respectively. Additionally, spoilage microorganisms, including Chryseobacterium , Propionibacterium , and Flavobacterium , and pathogenic bacteria, including Ochrobactrum anthropi and Sphingomonas , were more prevalent in horse and yak milk, whereas probiotic lactic acid bacteria (LAB), such as Leuconostoc , Lactococcus , or Lactobacillus , were more prevalent in goat, donkey, and camel milk. Furthermore, Moraxella was abundantly present in goat, camel, and yak milk, Acinetobacter was more abundant in camel milk, and Pseudomonas was relatively abundant in sheep and donkey milk. Overall, specific harmful microorganisms and probiotic lactic acid bacteria were found in the raw milk samples obtained from different animals, which provided a basis for preventing and controlling the growth of harmful bacteria, as well as investigating probiotic resources in raw milk. [ABSTRACT FROM AUTHOR]

Dyed wood is prone to photoaging when exposed to UV irradiation which decreases its decorative effect and service life. Holocellulose, as the main component of dyed wood, has a photodegradation behavior which is still unclear. To investigate the effect of UV irradiation on chemical structure and microscopic morphology changes of dyed wood holocellulose, Maple birch (Betulacostata Trautv) dyed wood and holocellulose were exposed to UV accelerated aging treatment; the photoresponsivity includes crystallization, chemical structure, thermal stability, and microstructure were studied. Results showed that UV radiation has no significant effect on the lattice structure of dyed wood fibers. The wood crystal zone diffraction 2θ and layer spacing was basically unchanged. With the UV radiation time extension, the relative crystallinity of dyed wood and holocellulose showed a trend of increasing first and then decreasing, but the overall change was not significant. The relative crystallinity change range of the dyed wood was not more than 3%, and the dyed holocellulose was not more than 5%. UV radiation caused the molecular chain chemical bond in the non-crystalline region of dyed holocellulose to break, the fiber underwent photooxidation degradation, and the surface photoetching feature was prominent. Wood fiber morphology was damaged and destroyed, finally leading to the degradation and corrosion of the dyed wood. Studying the photodegradation of holocellulose is helpful to understand the photochromic mechanism of dyed wood, and, further, to improve its weather resistance. [ABSTRACT FROM AUTHOR]

Human gut microbiota interfere with host development and aging. Bifidobacterium is a microbial genus found in the human digestive tract that has probiotic activities such as improving constipation and enhancing immunity. The species and numbers present change with age, but there has been limited research on probiotic gut microbiota at specific ages. This study analyzed the distribution of 610 bifidobacteria in subjects in several age groups (0−17, 18−65, and 66−108 y) using 486 fecal samples and determined the distribution of glycoside hydrolases based on genetic analysis of strains representing 85% of the Bifidobacterium species abundance in each age group. 6'-Sialyllactose is a major component of acidic breast milk oligosaccharides, which can promote human neurogenesis and bifidobacteria growth. Using genotypic and phenotypic association analysis, we investigated the utilization of 6'-sialyllactose by six B. bifidum strains isolated from subjects 0–17 and 18–65 y. A comparative genomic analysis of the six B. bifidum strains revealed differences in genomic features across age groups. Finally, the safety of these strains was evaluated by antibiotic gene and drug resistance phenotype analysis. Our results reveal that the distribution of glycoside hydrolase genes in B. bifidum varies with age, thus affecting the phenotypic results. This provides important insights for the design and application of probiotic products for different ages. [ABSTRACT FROM AUTHOR]

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Psychrophiles inhabiting various cold environments are regarded as having evolved diverse physiological and molecular strategies, such as the accumulation of trehalose to alleviate cold stress. To investigate the possible contributions of trehalose metabolism-related enzymes to cold-adaption in psychrotrophic bacteria and enrich the resource bank of trehalose hydrolysis enzymes, a novel cold-adapted GH15 GA-like trehalase (MpTre15A) from psychrotolerant Microbacteriumphyllosphaerae LW106 isolated from glacier sediments was cloned and characterized. The recombinant MpTre15A from M. phyllosphaerae LW106 was expressed and purified in Escherichia coli BL21(DE3). The purified MpTre15A functioned as a hexamer and displayed maximal activity at pH 5.0 and 50 °C. Substrate specificity assay proved MpTre15A only showed hydrolytic activity toward α,α-trehalose. Site-directed mutation verified the key catalytic sites of Glu392 and Glu557 in MpTre15A. The kcat and kcat/Km values of MpTre15A at 4 °C (104.50 s−1 and 1.6 s−1 mM−1, respectively) were comparable to those observed for thermophilic GH15 trehalases at 50 °C, revealing its typical cold-adaptability. MpTre15A showed a trehalose conversion rate of 100% and 99.4% after 10 min and 15 min of incubation at 50 °C and 37 °C, respectively. In conclusion, this novel cold-adapted α,α-trehalase MpTre15A showed potential application for developing therapeutic enzymes, enzyme-based biosensors, and enzyme additives in the fermentation industry. [ABSTRACT FROM AUTHOR]

In order to contribute to our understanding of Acidithiobacillus taxonomy, we determined 16S rDNA sequences and the 16S-23S internally transcribed spacer (ITS) sequence of 35 Chinese Acidithiobacillus isolates and three reference strains representing three validly described species and used them to construct phylogenetic trees. The two phylogenetic trees were roughly similar topologically, and Acidithiobacillus strains were assigned to eight phylogenetic groups. In addition, the results of phylogenetic analysis were consistent with those obtained by randomly amplified polyrnorphic DNA (RAPD) cluster analysis. Compared with a phylogenetic tree based on the 16S rRNA sequences, the ITS tree showed more clearly the inter- and intraspecific genealogical relationships of the genus Acidithiobacillus. Similarity values of the ITSs varied from 60.5% to 84.7% between representative strains of different species, and the maximum level of ITS divergence between strains belonging to the same species was 13%. Coupling phylogenetic analysis and phenotypic characteristics, we concluded that at least each of the three Acidithiobacillus ferrooxidans phylogenetic groups should be considered a separate subspecies, and that five sulfur-oxidizing Chinese Acidithiobacillus-like isolates represent one or two new species of the genus Acidithiobacillus. The ITS may be a potential target for the development of fluorescent in situ hybridization probes for more accurately detecting distinct ecotypes of Acidithiobacillus strains and other closely related sulfur-oxidizing bacteria.

Acrylamide, a II A carcinogen, widely exists in fried and baked foods. L-asparaginase can inhibit acrylamide formation in foods, and enzymatic stability is the key to its application. In this study, the Escherichia coli L-asparaginase (ECA) stable variant, D60W/L211R/L310R, was obtained with molecular dynamics (MD) simulation, saturation mutation, and combinatorial mutation, the half-life of which increased to 110 min from 60 min at 50 °C. Furthermore, the working temperature (maintaining the activity above 80%) of mutation expanded from 31 °C–43 °C to 35 °C–55 °C, and the relative activity of mutation increased to 82% from 65% at a pH range of 6–10. On treating 60 U/mL and 100 U/g flour L-asparaginase stable mutant (D60W/L211R/L310R) under uncontrolled temperature and pH, the acrylamide content of potato chips and bread was reduced by 66.9% and 51.7%, which was 27% and 49.9% higher than that of the wild type, respectively. These results demonstrated that the mutation could be of great potential to reduce food acrylamide formation in practical applications. [ABSTRACT FROM AUTHOR]

The maternal gut is thought to be the principal source of potential probiotic bacteria in the infant gut during the lactation stage. It is not clear whether facultative symbiont lactobacilli strictly follow vertical transmission from mother to infant and display the ethnic specificity in terms of species and strain composition in mother–infant cohorts. In the present study, a total of 16 former Lactobacillus species (365 strains) and 11 species (280 strains) were retrieved from 31 healthy mother–infant pairs of two ethnic groups, which have never intermarried, respectively. The result showed that the composition and number of Lactobacillus species between the two ethnic groups varied. Among 106 Lacticaseibacillus paracasei strains isolated, 64 representative strains were classified into 27 sequence types (ST) by means of multilocus sequence typing (MLST), of which 20 STs derived from 33 Uighur strains and 7 STs from 31 Li strains, and no homologous recombination event of genes was detected between strains of different ethnic groups. A go-EBURST analysis revealed that except for a few mother–infant pairs in which more than one STs were detected, L. paracasei isolates from the same mother–infant pair were found to be monophyletic in most cases, confirming vertical transfer of Lactobacillus at the strain level. More notably, L. paracasei isolates from the same ethnic group were more likely than strains from another to be incorporated into a specific phylogenetic clade or clonal complex (CC) with similar metabolic profile of glycan, supporting the hypothesis of ethnic specificity to a large degree. Our study provides evidence for the development of personalized probiotic tailored to very homogenous localized populations from the perspective of maternal and child health. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 gro EL 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 gro EL gene proved to be a very effective target for the depth resolution of Bifidobacterium community by high-throughput sequencing technologies. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Acidithiobacillus ferrooxidans YNTRS-40 (A. ferrooxidans) is a chemolithoautotrophic aerobic bacterium isolated from Tengchong hot springs, Yunnan Province, China, with a broad growth pH range of 1.0–4.5. This study reports the genome sequence of this strain and the information of genes related to the adaptation of diverse stresses and the oxidation of ferrous iron and sulfur. Results showed that YNTRS-40 possesses chromosomal DNA (3,209,933-bp) and plasmid DNA (47,104-bp). The complete genome of 3,257,037-bp consists of 3,349 CDS genes comprising 6 rRNAs, 52 tRNAs, and 6 ncRNAs. There are many encoded genes associated with diverse stresses adaptation and ferrous iron and sulfur oxidation such as rus operon, res operon, petI, petII, sqr, doxDA, cydAB, and cyoABCD. This work will provide essential information for further application of A. ferrooxidans YNTRS-40 in industry. [ABSTRACT FROM AUTHOR]

Chickpea milk is a nutrient-rich plant-based milk, but its pronounced beany flavour limits consumer acceptance. To address this issue, chickpea milk was fermented using two strains of Lactiplantibacillus plantarum, FMBL L23251 and L23252, which efficiently utilize chickpea milk. L. plantarum FMBL L23251 demonstrated superior fermentation characteristics. Fermentation with L. plantarum FMBL L23251 resulted in a 1.90-fold increase in vitamin B3 (271.66 ng/ml to 516.15 ng/ml) and a 1.58-fold increase in vitamin B6 (91.24 ng/ml to 144.16 ng/ml) through the L-aspartic acid pathway and the 1-deoxy-D-xylulose-5-phosphate (DXP)-independent pathway, respectively. Furthermore, L. plantarum FMBL L23251 effectively removed beany flavours due to its enhanced pathway for pyruvate metabolism. The main aldehydes are converted into corresponding alcohols or acids, resulting in 87.74 % and 96.99 % reductions in hexanal and 2-pentyl-furan, respectively. In summary, the fermentation of L. plantarum FMBL L23251 generated fermented chickpea milk that is rich in B vitamins and provides a better flavour. • L. plantarum FMBL L23251 boosts chickpea milk's vitamin B3 & B6 by 1.90 & 1.58 fold. • Fermentation with L. plantarum FMBL L23251 significantly reduces beany flavours like hexanal and 2-pentyl-furan. • Omics reveal L. plantarum FMBL L23251's pathways for flavour and B vitamin changes in chickpea milk. • Findings guide development of healthier, tastier plant-based milk alternatives like chickpea milk. [ABSTRACT FROM AUTHOR]

• B.animalis subsp.lactis HN-3 was suitable strain for EOJ fermentation. • Antioxidant capacities of EOJ were increased by Bifidobacteria fermentation. • Less-active bioconjugates of EOJ were decreased by Bifidobacteria fermentation. • High bioactive free form compounds were increased by Bifidobacteria fermentation. • Deglycosidation and demethylation were occurred during fermentation process. Elaeagnus angustifolia var. orientalis (L.)Kuntze fruit contains a large number of naturally occurring molecules present as glycoside, methylated, and methyl ester conjugates, which should be hydolysed or transformed to become bioactive forms. For this purpose, Bifidobacterium animalis subsp. lactis HN-3 was selected to ferment Elaeagnus angustifolia var. orientalis (L.)Kuntze fruit juice (EOJ). After fermentation, the total phenolic content (TPC) and antioxidant capacity of the EOJ increased significantly compared to the non-fermented EOJ. Using widely-targeted metabolomics analysis, polyphenolic compounds involved in the flavonoid biosynthetic pathway were determined to be up-regulated in the fermented EOJ. In addition, the metabolites generated by 8 deglycosidation, 5 demethylation, 5 hydrogenation, and 28 other reactions were detected in higher concentrations in the fermented EOJ compared to the non-fermented EOJ. Interestingly, these up-regulated metabolites have higher antioxidant and other biological activities than their metabolic precursors, which provide a theoretical basis for the development of Bifidobacterium- fermented plant products with stronger functional activities. [ABSTRACT FROM AUTHOR]

• 216 MFGM and 109 whey proteins were significantly difference between CB and CD. • These difference proteins were mainly related to immunity, inflammation and catalysis. • Proteins involved in PI3K/AKT signal pathway may attribute to the hypoglycemic effect. Camel milk is rich in nutrients and its impact on human medicine and nutrition cannot be ignored. We conducted an in-depth analysis of milk proteins obtained from two camel breed (Camelus bactrianus , CB and Camelus dromedarius , CD). Label-free proteomic technology was performed to analysis the MFGM and whey proteomes of CB and CD milk. In total, 1133 MFGM proteins and 627 whey proteins were identified from camel milk. Results revealed that 216 MFGM proteins and 109 whey proteins were significantly different between them. In addition, the cellular process, cell and binding were the predominately GO annotations of milk proteins. KEGG analysis shown that most proteins were involved in metabolic pathways. Furthermore, many proteins were found to be involved in PI3K/AKT signaling pathway, which could be the possible reason for hypoglycemic effect of camel milk. These results could provide a further understanding for unique biological characteristics of camel milk proteins. [ABSTRACT FROM AUTHOR]

The exponential growth of high-throughput sequencing (HTS) data on the microbial communities presents researchers with an unparalleled opportunity to delve deeper into the association of microorganisms with host phenotype. However, this growth also poses a challenge, as microbial data are complex, sparse, discrete, and prone to zero inflation. Herein, by utilizing 10 distinct counting models for analyzing simulated data, we proposed an innovative Bayesian zero-inflated negative binomial (ZINB) regression model that is capable of identifying differentially abundant taxa associated with distinctive host phenotypes and quantifying the effects of covariates on these taxa. Our proposed model exhibits excellent accuracy compared with conventional Hurdle and INLA models, especially in scenarios characterized by inflation and overdispersion. Moreover, we confirm that dispersion parameters significantly affect the accuracy of model results, with defects gradually alleviating as the number of analyzed samples increases. Subsequently applying our model to amplicon data in real multi-ethnic children cohort, we found that only a subset of taxa were identified as having zero inflation in real data, suggesting that the prevailing understanding and processing of microbial count data in most previous microbiome studies were overly dogmatic. In practice, our pipeline of integrating bacterial differential abundance in microbiome data and relevant covariates is effective and feasible. Taken together, our method is expected to be extended to the microbiota studies of various multi-cohort populations., Importance: The microbiome is closely associated with physical indicators of the body, such as height, weight, age and BMI, which can be used as measures of human health. Accurately identifying which taxa in the microbiome are closely related to indicators of physical development is valuable as microbial markers of regional child growth trajectory. Zero-inflated negative binomial (ZINB) model, a type of Bayesian generalized linear model, can be effectively modeled in complex biological systems. We present an innovative ZINB regression model that is capable of identifying differentially abundant taxa associated with distinctive host phenotypes and quantifying the effects of covariates on these taxa, and demonstrate that its accuracy is superior to traditional Hurdle and INLA models. Our pipeline of integrating bacterial differential abundance in microbiome data and relevant covariates is effective and feasible.

Little has been known about symbiotic relationships and host specificity for symbionts in the human gut microbiome so far. Bifidobacteria are a paragon of the symbiotic bacteria biota in the human gut. In this study, we characterized the population genetic structure of three bifidobacteria species from 58 healthy mother-infant pairs of three ethnic groups in China, geographically isolated, by Rep-PCR, multi-locus sequence analysis (MLSA), and in vitro carbohydrate utilization. One hundred strains tested were incorporated into 50 sequence types (STs), of which 29 STs, 17 STs, and 4 STs belong to B. longum subsp. longum , B. breve , and B. animalis subsp. lactis , respectively. The conspecific strains from the same mother-child pair were genetically very similar, supporting the vertical transmission of Bifidobacterium phylotypes from mother to offspring. In particular, results based on allele profiles and phylogeny showed that B. longum subsp. longum and B. breve exhibited considerable intraspecies genetic heterogeneity across three ethnic groups, and strains were clustered into ethnicity-specific lineages. Yet almost all strains of B. animalis subsp. lactis were incorporated into the same phylogenetic clade, regardless of ethnic origin. Our findings support the hypothesis of co-evolution between human gut symbionts and their respective populations, which is closely linked to the lifestyle of specific bacterial lineages. Hence, the natural and evolutionary history of Bifidobacterium species would be an additional consideration when selecting bifidobacterial strains for industrial and therapeutic applications., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Aihetanmu, Liang, Zhang, Luo, Zhang, Huang, Tian, Sun and Ni.)

Introduction: As prebiotics, oligosaccharides are frequently combined with Bifidobacterium to develop synbiotic products. However, a highly diverse gene repertoire of Bifidobacterium is involved in sugar catabolism, and even phylogenetically close species may differ in their sugar utilization capabilities. To further explore the mechanism underlying the differences in Bifidobacterium animalis subsp. lactis oligosaccharide metabolism., Methods: This study screened strains with differential oligosaccharide metabolism. Subsequently, these strains were subjected to genome-wide resequencing and RT-qPCR., Results: The resequencing results indicated that the subspecies of B. animalis subsp. lactis had a high genome similarity. The RT-qPCR results revealed that glycosidase genes exhibited consistency in the phenotype of metabolism at the transcriptional level; the better the growth of the strains on the oligosaccharides, the higher was the expression of glycosidase genes related to the oligosaccharides. Our results suggested that the differences in the gene transcription levels led to intraspecies differences in the ability of the strains to metabolize oligosaccharides even when they belonged to the same subspecies., Discussion: Future studies with more sample size could generalizable the conclusion to all B. animalis subsp. lactis strains, thus would lay the theoretical foundation for the utilization of the B. animalis subsp. lactis strain as probiotics and the development of synbiotic products., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Lan, Zhang, Xu, Kong, Zuo, Wang, Wang, Teng, Ni and Zhang.)

Elaeagnus moorcroftii Wall. ex Schlecht. (EWS) has extensive nutrients and functional active ingredients, which makes it an excellent potential substrate for fermentation. The improvement in the antioxidant activity of Elaeagnus moorcroftii Wall. ex Schlecht. juice (EWSJ) fermented by Bifidobacterium animalis subsp. lactis HN-3 (B.an3) could be attributed to the metabolism and biotransformation of plant-based products by the bacterial strain. To reveal the underlying mechanism, non-targeted metabolomics was applied in this study. After fermentation, the structure of downregulated carbohydrates, amino acids, fatty acids, and flavonoids was changed by Bifidobacterium biotransformation (included four reductions, three hydrolyses, four isomerizations, three deglycosidations, and five other reactions). The structure of these converted upregulated products has a higher antioxidant ability to reduce free radicals than their precursors, such as the flavonoids in the form of hydrolyzed conjugates, amino acids with multiple sulfhydryls or hydroxys, carbohydrates with reactive oxygen on benzene rings and fatty acids with unsaturated bonds, short chains, and glycosides. These findings shed light on the mechanism of the metabolism and biotransformation of EWSJ by B.an3, facilitate the study of the interaction between probiotics and fermented plant-based products, and provide a theoretical basis for the development of Bifidobacterium -fermented plant products with stronger functional activities.

Colostrum represents an important source for the transfer of important commensal bacteria from mother to newborn and has a strong impact on the newborn's health after birth. However, the composition of the colostrum microbiome is highly heterogeneous due to geographic factors and ethnicity (maternal, cultural, and subsistence factors). By analyzing the colostrum 16S rRNA gene full-length sequencing dataset in 97 healthy mothers (60 from Han, 37 from Li) from the Hainan island of China, we showed that the ethnic differences of the colostrum microbiome in a maternal cohort with different ethnic origins shared physical geography. Results indicated that the richness of microbial community in colostrum of Han women was higher than that of Li women, but there was no significant difference in Shannon index and invsimpson index between the two groups. Visualization analysis based on the distance showed an obvious ethnicity-associated structural segregation of colostrum microbiota. The relative abundance of Firmicutes was higher in the microbiota of the Han group than in Li's, while Proteobacteria was on the contrary. At the genus level, the most dominant members of the Han and Li ethnic groups were Acinetobacter and Cupriavidus , two common environmental bacteria, respectively, although skin-derived Staphylococcus and Streptococcus were still subdominant taxa. Cupriavidus lacunae was the most dominant species in the Li group, accounting for 26.10% of the total bacterial community, but only 3.43% for the Han group with the most dominant Staphylococcus petrasii (25.54%), indicating that human colostrum microbiome was more susceptible to local living environmental factors. Hence, the ethnic origin of individuals may be an important factor to consider in human milk microbiome research and its potential clinical significance during the perinatal period in ethnic-diverse societies, even within a small geographic scale., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Xie, Zhang, Ni and Peng.)

Background: Epithelial-to-mesenchymal transition (EMT) is required for renal fibrosis, which is a characteristic of diabetic nephropathy (DN). Our previous study demonstrated that fibroblast growth factor 21 (FGF21) prevented DN associated with the suppressing renal connective tissue growth factor expression, a key marker of renal fibrosis. Therefore, the effects of FGF21 on renal fibrosis in a DN mouse model and the underlying mechanisms were investigated in this study., Methods: Type 1 diabetes mellitus was induced in C57BL/6J mice by intraperitoneal injections of multiple low doses of streptozotocin. Then, diabetic and non-diabetic mice were treated with or without FGF21 in the presence of pifithrin-α (p53 inhibitor) or 10-[4'-(N,N-Diethylamino)butyl]-2-chlorophenoxazine hydrochloride (10-DEBC) hydrochloride (Akt inhibitor) for 4 months., Results: DN was diagnosed by renal dysfunction, hypertrophy, tubulointerstitial lesions, and glomerulosclerosis associated with severe fibrosis, all of which were prevented by FGF21. FGF21 also suppressed the diabetes-induced renal EMT in DN mice by negatively regulating transforming growth factor beta (TGF-β)-induced nuclear translocation of Smad2/3, which is required for the transcription of multiple fibrotic genes. The mechanistic studies showed that FGF21 attenuated nuclear translocation of Smad2/3 by inhibiting renal activity of its conjugated protein p53, which carries Smad2/3 into the nucleus. Moreover pifithrin-α inhibited the FGF21-induced preventive effects on the renal EMT and subsequent renal fibrosis in DN mice. In addition, 10-DEBC also blocked FGF21-induced inhibition of renal p53 activity by phosphorylation of mouse double minute-2 homolog (MDM2)., Conclusion: FGF21 prevents renal fibrosis via negative regulation of the TGF-β/Smad2/3-mediated EMT process by activation of the Akt/MDM2/p53 signaling pathway., Competing Interests: No potential conflict of interest relevant to this article was reported., (Copyright © 2020 Korean Diabetes Association.)

Acidithiobacillus ferrooxidans YNTRS-40 ( A. ferrooxidans ) is a chemolithoautotrophic aerobic bacterium isolated from Tengchong hot springs, Yunnan Province, China, with a broad growth pH range of 1.0-4.5. This study reports the genome sequence of this strain and the information of genes related to the adaptation of diverse stresses and the oxidation of ferrous iron and sulfur. Results showed that YNTRS-40 possesses chromosomal DNA (3,209,933-bp) and plasmid DNA (47,104-bp). The complete genome of 3,257,037-bp consists of 3,349 CDS genes comprising 6 rRNAs, 52 tRNAs, and 6 ncRNAs. There are many encoded genes associated with diverse stresses adaptation and ferrous iron and sulfur oxidation such as rus operon, res operon, petI , petII , sqr , doxDA , cydAB , and cyoABCD . This work will provide essential information for further application of A. ferrooxidans YNTRS-40 in industry.

The aim of the present study was to determine the repairing effects of intercellular adhesion molecule (ICAM)-1-expressing mesenchymal stem cells (MSCs) in mice with autoimmune thyroiditis. Following induction of an experimental autoimmune thyroiditis (EAT) model, mice were randomly divided into the following groups (n=10 each): i) Normal control; and experimental groups that were subject to EAT induction, including ii) EAT model; and iii) primary MSC; iv) C3H10T1/2/MSC; v) C3H10T1/2-MIGR1/MSC; and vi) C3H10T1/2-MIGR1-ICAM-1/MSC, which were all administered the relevant cells. MSCs were administered via the caudal vein. A blood sample was harvested from the angular vein of each animal 28 days post-treatment and ELISA was used to determine the serum total triiodothyronine, total thyroxine (T4), thyroid-stimulating hormone (TSH), anti-thyroid peroxidase (TPOAb), anti-thyroid microsomal (TMAb) and anti-thyroglobulin (TGAb) antibodies. Hematoxylin and eosin staining was performed to evaluate injury of the thyroid gland by determining the size of the follicle, inflammatory infiltration, colloidal substance retention and epithelial injury. Reverse transcription-quantitative polymerase chain reaction was performed to determine the mRNA expression of interleukin (IL)-4, IL-10, IL-17 and interferon (INF)-γ. Western blot analysis was performed to determine the expression of p38 mitogen-activated protein kinase (p38) and extracellular signal-regulated kinase (ERK). To observe cellular migration in vivo , mice were divided into the following groups, (n=10 each), which were subject to EAT induction: i) CM-DiI-labeled primary MSC; ii) CM-DiI-labeled C3H10T1/2/MSC; iii) CM-DiI-labeled C3H10T1/2-MIGR1/MSC; and iv) CM-DiI-labeled C3H10T1/2-ICAM-1/MSC, which were all administered the relevant cells via the caudal vein. C3H10T1/2-ICAM-1/MSCs were able to ameliorate the expression of T4, TSH, TPOAb, TMAb and TGAb in vivo , attenuate thyroid follicle injury and decrease the splenic index in mice. They were also able to ameliorate the mRNA expression of IL-4, IL-10, IL-17 and INF-γ, and the modulation of the P38 and ERK-signaling pathways in the mouse spleen. Furthermore, ICAM-1 overexpression was able to modulate the nesting of MSCs in the thyroid gland and lung. These findings suggest that C3H10T1/2-ICAM-1/MSC may affect the differentiation, proliferation and migration of immunocytes through modulating the p38 and ERK signaling pathways, and that ICAM-1 may modulate the immunoregulatory effects of MSCs by affecting the migration of MSCs in vivo .