Haiyan Xu's research while affiliated with Inner Mongolia Agricultural University and other places

Publications (51)

Article
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A large number of microbial genomes have already been identified from the human gut microbiome, but the understanding of the role of the low-abundance species at the individual level remains challenging, largely due to the relatively shallow sequencing depth used in most studies. To improve genome assembling performance, a HiSeq-PacBio hybrid, ultr...
Preprint
Full-text available
A large number of microbial genomes have already been identified from the human gut microbiome, but the understanding of the role of the low-abundance species at the individual level remains challenging, largely due to the relatively shallow sequencing depth used in most studies. To improve genome assembling performance, a HiSeq-PacBio hybrid, ultr...
Article
Full-text available
Purpose Irritable bowel syndrome (IBS) is a functional bowel disorder. This study aimed to assess the effect of a probiotic product (containing Lactobacillus casei Zhang, Lactobacillus plantarum P-8, and Bifdobacterium animalis subsp. lactis V9) as an adjunct to a routine regimen in IBS management. Methods Forty-five patients with IBS were randomi...
Article
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Abstract There is a close relationship between the gut microbiome and health in humans including regulation of immunity and energy metabolism. This study investigated differences in the gut microbiome of herdsmen from two regions: Hongyuan pasture in Sichuan and Xilingol pasture in Inner Mongolia. We found significant differences in the gut microbi...
Article
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Chronic inflammation is a risk factor for colorectal cancer, and inflammatory cytokines secreted from inflammatory cells and active oxygen facilitate tumorigenesis. Intestinal bacteria are thought to regulate tumorigenesis. The longer the breastfeeding period, the lower is the risk of inflammatory bowel disease. Here, we investigated preventive eff...
Article
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The early-life gut microbiota is associated with potential development of diseases in adulthood. The sterile womb paradigm has been challenged by recent reports that revealed the presence of the meconium, amniotic fluid, and placenta microbiome. This study aimed to explore the maternal origin of the microbiota of neonate meconium by using the PacBi...
Article
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This was a pilot study aiming to evaluate the effects of probiotics as adjunctive treatment for ulcerative colitis (UC). Twenty-five active patients with UC were assigned to the probiotic (n = 12) and placebo (n = 13) groups. The probiotic group received mesalazine (60 mg kg-1 day-1 ) and oral probiotics (containing Lactobacillus casei Zhang, Lacto...
Article
Full-text available
Purpose Human colon inflammation is associated with changes in the diverse and abundant microorganisms in the gut. As important beneficial microbes, Lactobacillus contributes to the immune responses and intestinal integrity that may alleviate experimental colitis. However, the mechanisms underlying probiotic benefits have not been fully elucidated....
Article
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Background: Koumiss is a naturally fermented mare's milk. Over recent decades, numerous studies have revealed the diversity of lactic acid bacteria in koumiss. However, there is limited information available regarding its secondary major component yeast profile. Results: A total of 119 bacterial and 36 yeast species were identified among the 14...
Preprint
Full-text available
Background Koumiss is a naturally fermented mare’s milk. Over recent decades, numerous studies have revealed the diversity of lactic acid bacteria in koumiss. However, there is limited information available regarding its secondary major component yeast profile. Results A total of 119 bacterial and 36 yeast species were identified among the 14 koumi...
Preprint
Koumiss, a naturally fermented mare’s milk with a distinctive flavor, has been consumed for thousands of years by Mongolian people. To clarify the contribution of microbiota to the taste of koumiss, bacterial and yeast diversity in koumiss were investigated by single-molecule real-time sequencing; the organic acid content was quantified by HPLC, an...
Preprint
Full-text available
Background Koumiss is a naturally fermented mare’s milk. Over recent decades, numerous studies have revealed the diversity of lactic acid bacteria in koumiss. However, there is limited information available regarding its secondary major component yeast profile. Results A total of 119 bacterial and 36 yeast species were identified among the 14 koumi...
Article
The aim of the present study was to evaluate the effects of probiotics on the composition and function of the gut microbiota in dogs with diarrhoea. Forty dogs with diarrhoea were randomly allocated to the treatment group or control group. Probiotics, containing Lactobacillus casei Zhang, Lactobacillus plantarum P-8, and Bifdobacterium animalis sub...
Article
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Probiotics have been used successfully to promote human and animal health, but only limited studies have focused on using probiotics to improve the health of hosts of different age. Canine microbiome studies may be predictive of results in humans because of the high structural and functional similarity between dog and human microbiomes. A total of...
Article
Goat milk powder is a nutritious and easy-to-store product that is highly favored by consumers. However, the presence of contaminating bacteria and their metabolites may significantly affect the flavor, solubility, shelf life, and safety of the product. To comprehensively and accurately understand the sanitary conditions in the goat milk powder pro...
Article
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The effects of probiotics on host gastrointestinal health have become an area of particular interest in the field of probiotic research. However, the impact of the host intestinal environment on genomic changes in probiotic organisms remains largely unknown. To investigate, Lactobacillus plantarum P-8, a well-studied probiotic bacterium, was consum...
Article
This work developed a 16S rRNA-PacBio Single Molecule Real-Time (SMRT) sequencing-based method to identify and track the bacterial community of milk powder (MP) from two kinds of production settings, i.e., small-scale production contained within an in-house environment (minimal milk storage before pasteurization, milk concentration, and spray dryin...
Article
Background: Traditional Chongqing radish paocai fermented with aged brine is considered to have the most intense flavor and authentic taste. Eight "Yanzhi" (red, RRPB group) and "Chunbulao" (white, WRPB) radish paocai brine samples were collected from Chongqing peasant households, and the diversity and community structures of bacteria present in t...
Article
Probiotics administration can improve host health. This study aims to determine the effects of probiotics (Lactobacillus casei Zhang and Lactobacillus plantarum P-8) administration on milk production, milk functional components, milk composition, and fecal microbiota of dairy cows. Variations in the fecal bacteria microbiota between treatments were...
Article
Dalian sea cucumber, Yantai sea cucumber, and Weihai sea cucumber, which belong to Apostichopus japonicus, are protected as geographical indications in China based on their high nutritional values and medical propertys. The 26 samples, including Dalian sea cucumbers (9 samples) in Liaoning province, Yantai sea cucumbers (9 samples), and Weihai sea...
Article
As important lactic acid bacteria, Enterococcus species are widely used in the production of fermented food. However, as some strains of Enterococcus are opportunistic pathogens, their safety has not been generally accepted. In recent years, a large number of new species have been described and classified within the genus Enterococcus, so a better...
Article
Koji is a kind of Japanese traditional fermented starter that has been used for centuries. Many fermented foods are made from koji, such as sake, miso, and soy sauce. This study used the single molecule real-time sequencing technology (SMRT) to investigate the bacterial and fungal microbiota of 3 Japanese koji samples. After SMRT analysis, a total...
Article
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Gut microbiota is a determining factor in human physiological functions and health. It is commonly accepted that diet has a major influence on the gut microbial community, however, the effects of diet is not fully understood. The typical Mongolian diet is characterized by high and frequent consumption of fermented dairy products and red meat, and l...
Article
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The incidence of colon cancer has increased considerably and the intestinal microbiota participate in the development of colon cancer. We showed that the L. casei Zhang or vitamin K2 (Menaquinone-7) intervention significantly alleviated intestinal tumor burden in mice. This was associated with increased serum adiponectin levels in both treatments....
Article
Sichuan paocai, a traditional Chinese fermented vegetable, is rife with lactic acid bacteria (LAB). However, the precise bacterial profiles of home-made Sichuan paocai brine (HSPB) remain unclear. In this study, the bacterial compositions of 38 aged HSPB samples with varying titratable acidity (TA) were determined by SMRT sequencing of the full-len...
Article
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Background In Kazakhstan, traditional artisanal cheeses have a long history and are widely consumed. The unique characteristics of local artisanal cheeses are almost completely preserved. However, their microbial communities have rarely been reported. The current study firstly generated the Single Molecule, Real-Time (SMRT) sequencing bacterial div...
Article
The gut microbiota of Mongolian hosts has distinctive characteristics due to their meat- and dairy-oriented daily diets and unique genotype. The aim of the present study was to investigate the effect of switching from the typical high protein and fat Mongolian diets to carbohydrate-rich meals composed principally of wheat, rice and naked oats on th...
Article
Infant formula (IF) requires a strict microbiological standard because of the high vulnerability of infants to foodborne diseases. The current study used the PacBio single molecule real-time (SMRT) sequencing platform to generate full-length 16S rRNA-based bacterial microbiota profiles of thirty Chinese domestic and imported IF samples. A total of...
Article
Koumiss is considered as a complete dairy product high in nutrients and with medicinal properties. The bacterial communities involved in production of koumiss play a crucial role in the fermentation cycle. To reveal bacterial biodiversity in koumiss and the dynamics of succession in bacterial populations during fermentation, 22 samples were collect...
Article
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The present study applied the PacBio single molecule, real-time sequencing technology (SMRT) in evaluating the quality of silage production. Specifically, we produced four types of Medicago sativa silages by using four different lactic acid bacteria-based additives (AD-I, AD-II, AD-III and AD-IV). We monitored the changes in pH, organic acids (incl...
Article
Lactobacillus casei is a lactic acid bacterium used in manufacturing of many fermented food products. To investigate the genetic diversity and population biology of this food-related bacterium, 224 Lb. casei isolates and 5 reference isolates were examined by multilocus sequence typing (MLST). Among them, 224 Lb. casei isolates were isolated from ho...
Article
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Lactobacillus plantarum is a lactic acid bacterium (LAB) of considerable industrial interest since it has an important role in the production of fermented food. In the present study, the genetic diversity and population structure within 186 L. plantarum isolates was determined based on a novel MLST scheme employing eight housekeeping genes. These i...
Article
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Background: Streptococcus thermophilus is a major dairy starter used for manufacturing of dairy products. In the present study, we developed a multilocus sequence typing (MLST) scheme for this important food bacterium. Sequences of 10 housekeeping genes (carB, clpX, dnaA, murC, murE, pepN, pepX, pyrG, recA, and rpoB) were obtained for 239 S. therm...
Article
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The Pacific Biosciences (Menlo Park, CA) single molecule, real-time sequencing technology (SMRT) was reported to have some advantages in analyzing the bacterial profile of environmental samples. In this study, the presence of bacterial contaminants in raw milk, UHT milk, and infant formula was determined by SMRT sequencing of the full length 16S rR...
Article
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Background Lactobacillus fermentum is economically important in the production and preservation of fermented foods. A repeatable and discriminative typing method was devised to characterize L. fermentum at the molecular level. The multilocus sequence typing (MLST) scheme developed was based on analysis of the internal sequence of 11 housekeeping ge...
Article
Lactobacillus helveticus is an economically important lactic acid bacterium used in industrial dairy fermentation. In the present study, the population structure of 245 isolates of L. helveticus from different naturally fermented dairy products in China and Mongolia were investigated using an multilocus sequence typing scheme with 11 housekeeping g...
Article
Leuconostoc mesenteroides strains play an important role in food fermentation. In this study, 136 strains from different dairy products in China and Mongolia were examined by multilocus sequence typing of 9 housekeeping genes. In total, 82 polymorphic sites were detected among the 9 loci. The number of polymorphic nucleotide sites varied between 4...
Article
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Structural profiling of healthy human gut microbiota across heterogeneous populations is necessary for benchmarking and characterizing the potential ecosystem services provided by particular gut symbionts for maintaining the health of their hosts. Here we performed a large structural survey of fecal microbiota in 314 healthy young adults, covering...
Article
Background To gain a deeper knowledge to the bacterial and fungal community diversity of home-made yoghurt from Zhaosu and Tekesi counties of Xinjiang in China, where relatively high proportion of ethnic minority population resides and their local home-made yoghurt are well-known.ResultsThe bacterial and fungal community diversity of 22 home-made y...
Article
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Background Economically, Leuconostoc lactis is one of the most important species in the genus Leuconostoc. It plays an important role in the food industry including the production of dextrans and bacteriocins. Currently, traditional molecular typing approaches for characterisation of this species at the isolate level are either unavailable or are n...
Article
To determine the genetic diversity and phylogenetic relationships among Lactococcus lactis isolates, 197 strains isolated from naturally homemade yogurt in 9 ethnic minority areas of 6 provinces of China were subjected to multilocus sequence typing (MLST). The MLST analysis was performed using internal fragment sequences of 12 housekeeping genes (c...
Article
Using the 16S rRNA, dnaA, murC and pyrG gene sequences, we identified the phylogenetic relationship among closely related Leuconostoc citreum species. Seven Leu. citreum strains originally isolated from sourdough were characterized by PCR methods to amplify the dnaA, murC and pyrG gene sequences, which were determined to assess the suitability as p...
Article
To compare six molecular methods for differentiation of Lactococcus lactis subsp. lactis and cremoris. Six molecular methods, such as 16S rRNA gene analysis, 16S-23S rRNA Intergenic spacer region polymorphism, Denaturing Gradient Gel Electrophoresis (DGGE), Random Amplified Polymorphic DNA (RAPD), Repetitive Extragenic Palindromic-PCR and Restricte...

Citations

... Metagenomic approaches such as metagenomeassembled genomes provide a direct assessment of the full suite of functional genes of the microbiome, although the results are dependent on sequencing depth (Durazzi et al. 2021). Previous metagenomic sequencing approaches were limited by low sequencing depth (e.g., Illumina HiSeq only), which are unable to capture low abundance microbial genomes, but a combination of long-read sequencing approaches (e.g., HiSeq-PacBio hybrid) can cover repetitive and low-coverage regions, increasing metagenomic assembly contiguity (Jin et al. 2022). Regardless of the specific microbial taxa present, the overall diversity of genes and subsequent metabolic functions can be used as a measure of resiliency (Xu et al. 2014). ...
... Since SMRT sequencing is currently inaccessible to most laboratories because of its high cost and laborious preparation procedure, researchers often work with the portable MinION device available from ONT . Although hybrid approach recovered high-quality MAGs from a complex aquifer system Overholt et al. (2020) and Jin et al. (2022) used MetaBAT2 to assemble 475 high-quality MAGs by HiSeq-PacBio hybrid, there were few reports on the assessment of different hybrid assemblers and Metagenome-assembled genome binning methods. ...
... Colitis caused by CRC can be alleviated via the abovementioned three methods. Xu et al. (2021) found in a study of Lactobacillus rhamnosus Probio-m9 that it can inhibit the expression of p-signal transducer and activator of transcription-3 and p-Akt, improve the balance of the intestinal flora, especially Akkermansia, Bifidobacterium, and Blautia, and suppress effects leading to CRC-related carcinogenesis. In particular, the study indicated that L. rhamnosus Probio-m9 can affect the metabolism of microbiota, especially glucose metabolism, and pointed out that glucose metabolism plays a far-reaching role as a driving force in the occurrence of tumors. ...
... A relatively common observation is that the number and activity of intestinal dominant bacteria in fecal samples from IBS is lower than in those from healthy control subjects, as well as the intestinal microbial diversity and the intestinal microecological stability [14,15].On the contrary, the ratio of Firmicutes, Bacteroidetes, and the number of potential intestinal pathogenic bacteria, such as Escherichia coli, Streptococcus, Rumen cocci, and Clostridium increased significantly [16,17]. Fecal microbiota transplantation (FMT) [18], probiotics [19], and antibiotic [20] therapy can effectively improve the symptoms of IBS patients, which also demonstrate the important role of gut microbiota in the pathogenesis of IBS. However, there still were some studies which found no significant difference in gut microbiota from IBS [21] and FMT was ineffective in the treatment of IBS [22]. ...
... Probiotics intervention is one of the treatment tools [164]. Administration of probiotic cocktail can improve microbiota dysbiosis and relieve the intestinal inflammation both in in human and animal models [165]. Mechanistically, probiotic enhanced the activity of a microbial enzyme in feces, resulting in increased release of taurine [119]. ...
... We also reported that the mothers of F2 TCDD /Fish pups had improved placental function and their offspring were less susceptible to early-life conditions, likely because this paternal dietary intervention improved sperm function, which translated to improved placental function [12]. Additionally, the placental phenotype has been suggested to contribute to the development of the infant gut microbiome as a consequence of fetal ingestion of amniotic fluid [31][32][33]. However, to our knowledge, ours is the first study to explore the neonatal microbiome following toxicant exposure of the father. ...
... The effect of this hybrid process can be explained mainly by the powerful heating property of the microwave (Zaker et al., 2019). Unlike classical heat transfer rules, microwave irradiation is generally known as the most preferred process in the systems in solvent (Sun et al., 2020;Tony and Mansour, 2020). As a result of the thermal effects of the microwave ...
... Spearman rank correlation analysis was used to explore the interactions between core microbes. For small intestine microbiota in GV and GVP, Ribosomal 16S rRNA genes were sequenced on the PacBio RS II instrument (Pacifc Biosciences, MA, USA) and analyzed according to our previous study [29]. ...
... The set of all these fragments is considered representative of the set of bacterial genomes present in the original microbiota. This technique is commonly used to identify probiotic species [34], and to determine the effects of probiotic consumption on the composition and function of gut microbiota [35]. Chen et al. [36] used shotgun metagenomics to study the effect of probiotic-induced microbiome modulation on intestinal inflammation. ...
... Xu et al. studied the effect of probiotics on the gut microbiota of dogs of different ages and found that the probiotic compound preparation had the most obvious effect on elderly dogs. Our probiotics can greatly boost beneficial bacteria (Faecalibacterium prausnitzii and Lactobacillus species), and alter the intestinal microbial composition of old dogs, promoting the transition of the gut microbiome of older dogs to a younger state (Xu et al. 2019). L. casei Zhang, isolated from traditional fermented horse milk, was the first lactic acid bacterium in China that had whole-genome sequencing ) and has extremely high genetic stability (Wang et al. 2017). ...