Publications by authors named "Weicheng Li"

47 Publications

The association between overweight/obesity and poor cognitive function is mediated by inflammation in patients with major depressive disorder.

J Affect Disord 2022 09 28;313:118-125. Epub 2022 Jun 28.

The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China; Guangdong Engineering Technology Research Center for Translational Medicine of Mental Disorders, Guangzhou, China. Electronic address:

Background: Cognitive dysfunction is a common and core feature of major depressive disorder (MDD). Evidences exerted a potentially harmful role of obesity and higher peripheral levels of inflammation in cognitive function, but few studies have explored whether markers of peripheral inflammation might mediate the association between overweight/obesity and deficits in cognitive function. Our study aimed to examine the cognitive function in MDD patients and clarify the effects of overweight/obesity and inflammatory cytokines on cognitive dysfunction in this population.

Method: We used a cross-sectional design in this study. A total of 265 patients with MDD were enrolled and divided into underweight, normal weight and overweight/obese groups. The MATRICS Consensus Cognitive Battery (MCCB) was administered to measure the cognition. Plasma levels of nineteen cytokines were measured using high sensitivity multiplex bead-based assays.

Results: We found overweight/obese MDD patients associated with higher plasma levels of tumor necrosis factor (TNF)-α, interleukin (IL)-8, and macrophage inflammatory protein (MIP)-1β and worse performance in speed of processing and working memory. The mediation analysis found higher levels of IL-8 (direct: β = -0.591 (95 % Confidence Interval (CI): -1.0 to -0.2), P = 0.002; indirect: β = 0.060 (95 % CI.: 0.0-0.2), P = 0.032) and TNF-α (direct: β = -0.589 (95 % CI.: -1.0 to -0.2), P = 0.002; indirect: β = 0.059 (95 % CI.: 0.1-0.2), P = 0.037) were associated with more deficits in speed of processing, and partially mediated the relationship between body mass index and speed of processing.

Conclusion: Our results suggest that elevated inflammation might be one biological mechanism underlying the link between higher body mass and deficits in processing speed in patients with MDD.
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http://dx.doi.org/10.1016/j.jad.2022.06.073DOI Listing
September 2022

Advances in Immune Microenvironment and Immunotherapy of Isocitrate Dehydrogenase Mutated Glioma.

Front Immunol 2022 13;13:914618. Epub 2022 Jun 13.

Department of Neurosurgery, The First Affiliated Hospital of Hainan Medical University, Haikou, China.

The tumor immune microenvironment and immunotherapy have become current important tumor research concerns. The unique immune microenvironment plays a crucial role in the malignant progression of isocitrate dehydrogenase (IDH) mutant gliomas. IDH mutations in glioma can inhibit tumor-associated immune system evasion of NK cell immune surveillance. Meanwhile, mutant IDH can inhibit classical and alternative complement pathways and directly inhibit T-cell responses by metabolizing isocitrate to D-2-Hydroxyglutaric acid (2-HG). IDH has shown clinically relevant efficacy as a potential target for immunotherapy. This article intends to summarize the research progress in the immunosuppressive microenvironment and immunotherapy of IDH-mutant glioma in recent years in an attempt to provide new ideas for the study of occurrence, progression, and treatment of IDH-mutant glioma.
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http://dx.doi.org/10.3389/fimmu.2022.914618DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9234270PMC
June 2022

Comparative genomic analysis revealed genetic divergence between Bifidobacterium catenulatum subspecies present in infant versus adult guts.

BMC Microbiol 2022 06 16;22(1):158. Epub 2022 Jun 16.

Key Laboratory of Dairy Biotechnology and Engineering (Inner Mongolia Agricultural University), Ministry of Education; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China.

Background: The two subspecies of Bifidobacterium catenulatum, B. catenulatum subsp. kashiwanohense and B. catenulatum subsp. catenulatum, are usually from the infant and adult gut, respectively. However, the genomic analysis of their functional difference and genetic divergence has been rare. Here, 16 B. catenulatum strains, including 2 newly sequenced strains, were analysed through comparative genomics.

Results: A phylogenetic tree based on 785 core genes indicated that the two subspecies of B. catenulatum were significantly separated. The comparison of genomic characteristics revealed that the two subspecies had significantly different genomic sizes (p < 0.05) but similar GC contents. The functional comparison revealed the most significant difference in genes of carbohydrate utilisation. Carbohydrate-active enzymes (CAZyme) present two clustering patterns in B. catenulatum. The B. catenulatum subsp. kashiwanohense specially including the glycoside hydrolases 95 (GH95) and carbohydrate-binding modules 51 (CBM51) families involved in the metabolism of human milk oligosaccharides (HMO) common in infants, also, the corresponding fucosylated HMO gene clusters were detected. Meanwhile, B. catenulatum subsp. catenulatum rich in GH3 may metabolise more plant-derived glycan in the adult intestine.

Conclusions: These findings provide genomic evidence of carbohydrate utilisation bias, which may be a key cause of the genetic divergence of two B. catenulatum subspecies.
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http://dx.doi.org/10.1186/s12866-022-02573-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9202165PMC
June 2022

Comparative genomic analysis revealed genetic divergence between Bifidobacterium catenulatum subspecies present in infant versus adult guts.

BMC Microbiol 2022 06 16;22(1):158. Epub 2022 Jun 16.

Key Laboratory of Dairy Biotechnology and Engineering (Inner Mongolia Agricultural University), Ministry of Education; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China.

Background: The two subspecies of Bifidobacterium catenulatum, B. catenulatum subsp. kashiwanohense and B. catenulatum subsp. catenulatum, are usually from the infant and adult gut, respectively. However, the genomic analysis of their functional difference and genetic divergence has been rare. Here, 16 B. catenulatum strains, including 2 newly sequenced strains, were analysed through comparative genomics.

Results: A phylogenetic tree based on 785 core genes indicated that the two subspecies of B. catenulatum were significantly separated. The comparison of genomic characteristics revealed that the two subspecies had significantly different genomic sizes (p < 0.05) but similar GC contents. The functional comparison revealed the most significant difference in genes of carbohydrate utilisation. Carbohydrate-active enzymes (CAZyme) present two clustering patterns in B. catenulatum. The B. catenulatum subsp. kashiwanohense specially including the glycoside hydrolases 95 (GH95) and carbohydrate-binding modules 51 (CBM51) families involved in the metabolism of human milk oligosaccharides (HMO) common in infants, also, the corresponding fucosylated HMO gene clusters were detected. Meanwhile, B. catenulatum subsp. catenulatum rich in GH3 may metabolise more plant-derived glycan in the adult intestine.

Conclusions: These findings provide genomic evidence of carbohydrate utilisation bias, which may be a key cause of the genetic divergence of two B. catenulatum subspecies.
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http://dx.doi.org/10.1186/s12866-022-02573-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9202165PMC
June 2022

Comparative Genomics Revealed Wide Intra-Species Genetic Heterogeneity and Lineage-Specific Genes of .

Microbiol Spectr 2022 06 10;10(3):e0243921. Epub 2022 May 10.

Key Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering; Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural Universitygrid.411638.9, Hohhot, China.

Akkermansia muciniphila has potential as a next-generation probiotic, but few previous studies attempted to analyze its intraspecies population diversity. In this study, we performed a comparative genomic analysis of 112 filtered genomes from the NCBI database. The populations formed three clades (A-C) on the phylogenetic tree, suggesting the existence of three genetic lineages though clades B and C were phylogenetically closer than clade A. The three clades also showed geographic-based clustering, different genetic characteristics, and clade-specific genes. Two putative functional genes ( and ) were specific to clade C due to genomic islands. These lineage-specific genes might be associated with differences in genomic features (number of phages/genomic islands, pan-core genome, recombination rate, genetic diversity) between genetic lineages. The carbohydrate utilization gene profile (particularly for glycolytic hydrolases and carbohydrate esterases) also varied between clades, suggesting different carbohydrate metabolism potential/requirements between genetic lineages. Our findings provide important implications for future research on . Akkermansia muciniphila has been widely accepted as part of the next generation of probiotics. However, most current studies on have focused on the application of type strain BAA835 in the treatment of diseases, while few studies have reported on the genomic specificity, population structure, and functional characteristics of species. By comparing the genomes of 112 strains from NCBI which met the quality control conditions, we found that the population could be divided into three main clades (clades A to C) and presented a certain regional aggregation. There are significant differences among the three clades in their genetic characteristics and functional genes (the type strain BAA835 was located in clade A), especially in genes related to carbohydrate metabolism. It should be mentioned that probiotics should be a concept at the strain level rather than at the gut species level, so the probiotic properties of need to be carefully interpreted.
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http://dx.doi.org/10.1128/spectrum.02439-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9241678PMC
June 2022

subsp. subsp. nov., a lactic acid bacterium isolated from naturally fermented dairy product.

Int J Syst Evol Microbiol 2022 May;72(5)

Key Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, PR China.

Two lactic acid bacterial strains (IMAU80584 and IMAU92037) were isolated from naturally fermented dairy products (kurut and yoghurt) in China and Russia. Based on sequence analysis of the 16S rRNA gene it was revealed that these strains belonged to . However, phylogenetic tree analyses of two housekeeping genes, (encoding RNA polymerase alpha subunit) and (encoding phenylalanyl-tRNA synthase alpha subunit), and 88 core genes, indicated the two strains were separated into an independent monophyletic branch from DSM 19907, forming an infra-specific subgroup. The average nucleotide identity and digital DNA-DNA hybridization values between IMAU80584 and DSM 19907 were 93.1 and 52.8 %, respectively. Strains IMAU80584 and IMAU92037 are distinguished from DSM 19907 because they have different polar lipids and fatty acids. The novel subgroup strains could not ferment gluconate potassium. The DNA G+C content of strain IMAU80584 was 42.3 mol%. The major cellular fatty acids were C, C 9t and summed feature 5 (C ante and/or C 6 and/or C 9c). Therefore, based on the results of polyphasic taxonomic analysis, IMAU80584 and IMAU92037 could be considered as a novel subspecies in the species with the proposed name subsp. subsp. nov. The type strain is IMAU80584 (=GDMCC 1.2566=JCM 34647).
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http://dx.doi.org/10.1099/ijsem.0.005359DOI Listing
May 2022

Genomics divergence of Lactococcus lactis subsp. lactis isolated from naturally fermented dairy products.

Food Res Int 2022 05 7;155:111108. Epub 2022 Mar 7.

Key Laboratory of Dairy Biotechnology and Engineering (Inner Mongolia Agricultural University), Ministry of Education; Key Laboratory of Dairy Products Processing,Ministry of Agriculture and Rural Affairs; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, InnerMongolia 010018, PR China. Electronic address:

Lactococcus lactis subsp. lactis (L. lactis subsp. lactis) is commonly found in naturally fermented dairy products (NFDPs). This subspecies is of high economic value due to its wide application in dairy industry. However, the genetic background and evolutionary history of L. lactis subsp. lactis are still poorly understood, analysis of its genetic background and functional genome will lay a genetic foundation for its application. This study analyzed the whole genomes of 227 novel L. lactis subsp. lactis isolated from NFDPs and investigated the genetic history of this subspecies from a population genetic perspective. These strains were classified into four phylogenetically distinct groups, which were likely derived from only a few wild ancestors through three divergence events, resulting in genetic and phenotypic divergence. Functional genomic analysis found that the divergence events caused strong lineage-specific selection for carbohydrate utilization and lactic acid production genes. Moreover, the time of the divergence coincided with mass migration of nomads due to climate change and decrease in average annual temperature, suggesting that these drastic environmental changes might be evolutionary drivers of the divergence. Genome-wide association analysis results showed that the single nucleic acid polymorphic loci we associated with pepF and CoiA genes were significantly correlated with fermentation capability, and based on this, a rapid screening model for potential starter strains was constructed. Our findings shed light on the evolutionary history and genomic diversity of NFDP-originated L. lactis subsp. lactis, and provide a new insight for screening strains with excellent characteristics.
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http://dx.doi.org/10.1016/j.foodres.2022.111108DOI Listing
May 2022

Pre-treatment Pain Symptoms Influence Antidepressant Response to Ketamine in Depressive Patients.

Front Psychiatry 2022 16;13:793677. Epub 2022 Mar 16.

The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China.

Background: Pain strongly coexists with depression. Ketamine has great analgesic and antidepressant effects, acting as a promising role in treating depression with pain. Few studies have evaluated impact of pain symptoms on antidepressant effect of ketamine infusions. Thus, present study investigated whether pain symptoms in individuals with depression moderate response to ketamine.

Methods: One hundred and four individuals with major depressive disorder and bipolar depression received six intravenous infusions of ketamine. The Montgomery-Åsberg Depression Rating Scale (MADRS) was administered at baseline, the next morning after each infusion and 2 weeks (Day 26) after the last infusion. Pain symptoms were collected at baseline using the short-form McGill Pain Questionnaire (SF-MPQ).

Results: The prevalence of pain in patients with depression was 48.8%. Mix model analyses showed that pre-treatment pain symptoms assessed by each domain of SF-MPQ significantly moderated antidepressant response to six infusions of ketamine from baseline to day 26 (all < 0.05). Then follow-up simple slopes analyses suggested that all patients across groups showed a significant symptomatic improvement after ketamine infusions (all < 0.05), and patients with severe pain (across all domains of SF-MPQ) had greater improvement in depressive symptoms than those with mild pain or non-pain (all < 0.05).

Conclusion: A significant and rapid improvement in depressive symptoms was observed in patients with depression and pain after ketamine treatment. Ketamine may be a novel and promising antidepressant preferentially for the therapy of depression with severe pain.
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http://dx.doi.org/10.3389/fpsyt.2022.793677DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8967176PMC
March 2022

Structure characterization, antioxidant capacity, rheological characteristics and expression of biosynthetic genes of exopolysaccharides produced by Lactococcus lactis subsp. lactis IMAU11823.

Food Chem 2022 Aug 26;384:132566. Epub 2022 Feb 26.

Key Laboratory of Dairy Biotechnology and Engineering (Inner Mongolia Agricultural University), Ministry of Education; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, PR China. Electronic address:

Exopolysaccharides (EPSs) from lactic acid bacteria have special functions and complex structures, but the function and structure of EPSs of the important dairy starter, Lactococcus (L.) lactis subsp. lactis, are less known. This study investigated the cytotoxicity, antioxidant capacities, rheological characteristics, chemical structure and expression of biosynthetic genes of EPSs of the L. lactis subsp. lactis IMAU11823. The EPSs showed strong reducing power and no cytotoxicity. EPS-1 comprised glucose and mannose (molar ratio of 7.01: 1.00) and molecular weight was 6.10 × 10 Da, while EPS-2 comprised mannose, glucose and rhamnose (7.45: 1.00: 2.34) and molecular weight was 2.93 × 10 Da. EPS-1 was a linear structure comprised two sugar residues, while EPS-2 was more complex, non-linear, and comprised eight sugar residues. In additions, our study proposed an EPS biosynthesis model for the IMAU11823 strain. The current findings have broadened the understanding of the formation, structure and function of complex EPSs of IMAU11823.
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http://dx.doi.org/10.1016/j.foodchem.2022.132566DOI Listing
August 2022

V5 and GFP Tagging of Viral Gene pp38 of Marek's Disease Vaccine Strain CVI988 Using CRISPR/Cas9 Editing.

Viruses 2022 02 21;14(2). Epub 2022 Feb 21.

Viral Oncogenesis Group, The Pirbright Institute, Pirbright, Guildford GU24 0NF, UK.

Marek's disease virus (MDV) is a member of alphaherpesviruses associated with Marek's disease, a highly contagious neoplastic disease in chickens. The availability of the complete sequence of the viral genome allowed for the identification of major genes associated with pathogenicity using different techniques, such as bacterial artificial chromosome (BAC) mutagenesis and the recent powerful clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-based editing system. Thus far, most studies on MDV genome editing using the CRISPR/Cas9 system have focused on gene deletion. However, analysis of the expression and interactions of the viral proteins during virus replication in infected cells and tumor cells is also important for studying its role in MDV pathogenesis. The unavailability of antibodies against most of the MDV proteins has hindered the progress in such studies. This prompted us to develop pipelines to tag MDV genes as an alternative method for this purpose. Here we describe the application of CRISPR/Cas9 gene-editing approaches to tag the phosphoprotein 38 (pp38) gene of the MDV vaccine strain CVI988 with both V5 and green fluorescent protein (GFP). This rapid and efficient viral-gene-tagging technique can overcome the shortage of specific antibodies and speed up the MDV gene function studies significantly, leading to a better understanding of the molecular mechanisms of MDV pathogenesis.
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http://dx.doi.org/10.3390/v14020436DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8879161PMC
February 2022

Complete genome sequence of ST, a potential probiotic strain with antibacterial properties.

J Anim Sci Technol 2022 Jan 31;64(1):183-186. Epub 2022 Jan 31.

College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China.

() ST was isolated from De'ang pickled tea in Yunnan Province, China. The genomes of strain ST were fully sequenced and analyzed using the PacBio RS II sequencing system. Our previous study has shown that ST is a potential probiotic strain. It had strong tolerance in the simulated artificial gastrointestinal tract, and in the antagonism tests, this strain showed strong antibacterial activity. Therefore, as a probiotic, it may be used in animal breeding. ST genome was composed of 1 circular chromosome and 7 plasmids. The length of the whole genome was 3320817 bp, and the annular chromosome size was 3058984 bp, guanine + cytosine (G ± C) content (%) was 44.76%, which contained 2945 protein-coding sequences (CDS). This study will contribute to a further comprehensive understanding of ST at the genomic level and provide a theoretical basis for its future application in animal breeding.
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http://dx.doi.org/10.5187/jast.2022.e7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8819325PMC
January 2022

Predictors of 4-week antidepressant outcome in patients with first-episode major depressive disorder: An ROC curve analysis.

J Affect Disord 2022 05 13;304:59-65. Epub 2022 Feb 13.

Department of Psychiatry, Department of Neurology, Affiliated Brain Hospital, Guangzhou Medical University, Guangzhou, China; Southern Medical University, Guangzhou, China. Electronic address:

Background: Pretreatment characteristics of patients, symptom and function could be associated with antidepressant treatment outcome, but its predictive ability is not adequate. Our study aimed to identify predictors of acute antidepressant efficacy in patients with first-episode Major Depressive Disorder (MDD).

Methods: 187 patients with first-episode MDD were included and assessed clinical symptoms, cognitive function and global functioning using the 17-item Hamilton Depression Inventory (HAMD-17), MATRICS Consensus Cognitive Battery (MCCB) and Global Assessment of Functioning (GAF). Participants received treatment with a SSRI (escitalopram or venlafaxine) for 4 weeks. Logistic regression was used to analyze the association between patients' characteristics, symptom profiles, cognitive performance, and global functioning and the antidepressant outcome at the end of 4 weeks, and ROC curve analysis was performed for predictive accuracy with area under the receiver operating curve (AUC).

Results: Antidepressant improvement, response and remission rate at week 4 was 87.7%, 64.7% and 42.8%, respectively. The combination of pretreatment clinical profiles, speed of processing and global functioning showed moderate discrimination of acute improvement, response and remission with AUCs of 0.863, 0.812 and 0.734, respectively.

Limitations: The major limitation of the present study is the study did not combine pharmacogenomics from the perspective of antidepressant drug metabolism.

Conclusion: Aside from the baseline clinical symptoms, cognitive function and global functioning could be predictors of acute treatment outcome in first episode MDD using escitalopram or venlafaxine. This relatively simple application based on clinical symptoms and function seems to be cost-effective method to identify individuals who are more likely to respond to antidepressant treatment.
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http://dx.doi.org/10.1016/j.jad.2022.02.029DOI Listing
May 2022

Targeted Deletion of Glycoprotein B Gene by CRISPR/Cas9 Nuclease Inhibits Type 3 in Dually Infected Marek's Disease Virus-Transformed Lymphoblastoid Cell Line MSB-1.

J Virol 2022 03 2;96(6):e0202721. Epub 2022 Feb 2.

The Pirbright Institutegrid.63622.33, Pirbright, Guildford, Surrey, United Kingdom.

Marek's disease virus (MDV) is a member of the genus Mardivirus in the subfamily . There are three different serotypes of MDV designated as MDV-1 ( type 2), MDV-2 ( type 3), and MDV-3 (Meleagrid herpesvirus 1, herpesvirus of turkeys, HVT). MDV-1 is the only serotype that induces Marek's disease (MD), a lymphoproliferative disorder resulting in aggressive T-cell lymphomas and paralytic symptoms. In the lymphomas and lymphoblastoid cell lines (LCL) derived from them, MDV establishes latent infection with limited viral gene expression. The latent viral genome in LCL can be activated by co-cultivation with chicken embryo fibroblast (CEF) monolayers. MSB-1, one of the first MDV-transformed LCL established from the splenic lymphoma, is distinct in harboring both the oncogenic MDV-1 and non-oncogenic MDV-2 viruses. Following the successful application of CRISPR/Cas9 editing approach for precise knockdown of the MDV-1 genes in LCL, we describe here the targeted deletion of MDV-2 glycoprotein B (gB) in MSB-1 cells. Due to the essential nature of gB for infectivity, the production of MDV-2 plaques on CEF was completely abolished in the MDV-2-gB-deleted MSB-1 cells. Our study has demonstrated that the CRISPR/Cas9 system can be used for targeted inactivation of the co-infecting MDV-2 without affecting the MDV-1 in the MSB-1 cell line. Successful inactivation of MDV-2 demonstrated here also points toward the possibility of using targeted gene editing as an antiviral strategy against pathogenic MDV-1 and other viruses infecting chickens. Marek's disease (MD) is a lymphoproliferative disease of chickens characterized by rapid-onset lymphomas in multiple organs and by infiltration into peripheral nerves, causing paralysis. Lymphoblastoid cell lines (LCL) derived from MD lymphomas have served as valuable resources to improve understanding of distinct aspects of virus-host interactions in transformed cells including transformation, latency, and reactivation. MDV-transformed LCL MSB-1, derived from spleen lymphoma induced by the BC-1 strain of MDV, has a unique feature of harboring an additional non-pathogenic MDV-2 strain HPRS-24. By targeted deletion of essential gene glycoprotein B from the MDV-2 genome within the MSB-1 cells, we demonstrated the total inhibition of MDV-2 virus replication on co-cultivated CEF, with no effect on MDV-1 replication. The identified viral genes critical for reactivation/inhibition of viruses will be useful as targets for development of disease resistance in chickens to avian pathogens.
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http://dx.doi.org/10.1128/jvi.02027-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8941929PMC
March 2022

Long-term outcomes of repeated ketamine infusions in patients with unipolar and bipolar depression: A naturalistic follow-up study.

J Affect Disord 2022 03 22;300:172-178. Epub 2021 Dec 22.

The First School of Clinical Medicine, Southern Medical University, Guangzhou, China; The Affiliated Brain Hospital of Guangzhou Medical University (Guangzhou Huiai Hospital), Guangzhou, China; Guangdong Engineering Technology Research Center for Translational Medicine of Metal Disorders, Guangzhou, China. Electronic address:

Objective: Ketamine was proven to have short-term antidepressant effects. There is a paucity of studies focused on the long-term outcomes of repeated infusions of ketamine. This study aimed to examine the long-term outcomes of repeated ketamine infusions in patients with unipolar and bipolar depression METHODS: One hundred and eight patients with unipolar and bipolar depression completed the repeated treatment phase (administered ketamine three times weekly over a 12-day) and entered a 9-month naturalistic follow-up phase. Assessments were obtained at week 2, month 6, and month 9 after the repeated treatment phase. The Patient Health Questionnaire-9 (PHQ-9) Scale and the Global Assessment of Functioning (GAF) Scale were used to assess depressive symptoms and global functional status, respectively.

Results: Seventy-one (65.7%) of patients completed the 9-month follow-up. On month 9, the response and remission rate were 80.3% and 78.9%, respectively. Among 56 patients who achieved response after the repeated treatment phase, 26 (46.4%) of patients sustained response during 9-month follow-up and their GAF score remained over 70. Sixteen patients relapsed during the 9-month follow-up and 14 (85.7%) of the relapse occurred during the first 2-week follow-up.

Limitation: The major limitation of this study is the open-label design.

Conclusions: This small sample study suggested that patients with unipolar and bipolar depression who response to repeated treatment with continued oral antidepressant may be a viable treatment option, and their global functional status improved with a follow-up. Relapse of depression tended to occur during the 2 weeks follow-up.
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http://dx.doi.org/10.1016/j.jad.2021.12.084DOI Listing
March 2022

Genomics landscape of 185 Streptococcus thermophilus and identification of fermentation biomarkers.

Food Res Int 2021 12 9;150(Pt A):110711. Epub 2021 Sep 9.

Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering; Inner Mongolia Agricultural University, Hohhot 010018, China. Electronic address:

Streptococcus (S.) thermophilus, an indispensable dairy starter, has been used in autochthonous as well as industrial milk fermentation. However, the genetic architecture underlying S. thermophilus traits and phenotypes is largely unknown. Here, we sequenced 185 S. thermophilus strains, isolated from natural fermented dairy products of China and Mongolia and used comparative genomic and genome wide association study to provide novel point for genetic architecture underlying its traits and phenotypes. Genome analysis of S. thermophilus showed association of phylogeny with environmental and phenotypic features and revealed clades with high acid production potential or with substantial genome decay. A few S. thermophilus isolated from areas with high chloramphenicol emissions had a chloramphenicol-resistant gene CatB8. Most importantly, we defined a growth score and identified a missense mutation G1118698T located at the gene AcnA that were both predictive of acidification capability of S. thermophilus. Our findings provide novel insight in S. thermophilus genetic traits, antibiotic resistant and predictive of acidification capability which both may had huge help in culture starter screening.
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http://dx.doi.org/10.1016/j.foodres.2021.110711DOI Listing
December 2021

Comparative genomics of in vitro and in vivo evolution of probiotics reveals energy restriction not the main evolution driving force in short term.

Genomics 2021 09 24;113(5):3373-3380. Epub 2021 Jul 24.

Key Laboratory of Dairy Biotechnology and Engineering (Inner Mongolia Agricultural University), Ministry of Education; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China. Electronic address:

Probiotics have attracted much attention because of their health-promoting effects, but little is known about the in vivo evolution of probiotics. This study analyzed the genome adaptation of the probiotic Lactiplantibacillus plantarum P-8 strain cultivated in ordinary and glucose restrictive growth media. Then, this study re-analyzed genomes of P-8 isolates recovered from the gut contents of subjects in two feeding trials (in rat and human). The sampling time points were similar to that of the in vitro evolution experiment, which might give parallel comparison of the in vitro and in vivo evolution processes. Our results showed that intra-individual specific microbial genomic variants of the original strain were detected in all human and some rat subjects. The divergent patterns of evolution within the host gastrointestinal tract suggested intra-individual-specific environmental adaptation. Based on comprehensive analysis of adapted-isolates recovered from these experiments, our results showed that the energy restriction was not the main driving force for evolution of probiotics. The individual-specific adaptation of probiotics might partially explain the varying extent of health effects seen between different individuals after probiotic consumption. In addition, the results suggest that probiotics should not only adapt to the environment of the birth canal, but also adapt to other species in the gut, revealing the Red Queen hypothesis in the process of intestinal flora.
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http://dx.doi.org/10.1016/j.ygeno.2021.07.022DOI Listing
September 2021

[Covalent organic framework functional materials and their applications in glycopeptide enrichment].

Se Pu 2021 Jun;39(6):588-598

School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China.

Protein glycosylation is among the most important post-translational modifications in living organisms and the research in the field of protein glycosylation continues to garner attention. Currently, the efficient separation and enrichment of glycoproteins and glycopeptides is the primary challenge of glycoproteomics research. The number of glycoproteins is small in complex biological samples. Moreover, the presence of highly-abundant, non-glycosylated, and modified peptides makes the detection of low-abundance glycopeptides more difficult. Therefore, efficient glycopeptide enrichment methods are required to improve the detection of these compounds. The development of highly selective glycopeptide enrichment tools is important to efficiently capture glycoproteins or glycopeptides at the molecular level. Compared with traditional glycopeptide-enriched materials, covalent organic framework materials have the advantages of large specific surface area and rich modification sites, thereby exhibiting great application potential in the field of glycopeptide enrichment. In this study, a novel covalent organic framework material (O-T-D-COFs) was prepared and applied for selective glycopeptide enrichment. We applied the solvothermal method, using 2,5-dimethoxy benzene-1,4-2 formaldehyde and 1,3,5-Tris(4-aminophenyl) benzene, to synthesize imino-based COFs. The Schiff base generated via copolymerization condensation reaction constitutes the framework of the material. Next, the synthesized intermediate material was oxidized to improve the enrichment performance of the material. The functional, specific glycopeptide-binding groups were modified on the COF channels and the structure of the material was characterized using scanning and transmission electron microscope, as well as infrared spectrum and solid-state nuclear magnetic resonance. The enrichment conditions comprised the loading and elution steps, including the optimization of the elution conditions. We could observe the clear profile of 32 glycopeptides derived from human serum immunoglobulin G (IgG) tryptic digests with a significantly improved signal-to-noise () ratio. We applied a complex sample system to verify the enrichment selectivity of the material when the molar ratios of the IgG and bovine serum albumin (BSA) tryptic digest mixtures reached 1∶50. In addition, we investigated the enrichment performance of the detection limit, enrichment capacity, recovery rate of the material, and the application potential in glycopeptides enrichment using real samples. The material showed a good detection limit (2.5 fmol/μL), an ideal enrichment capacity (120 mg/g), and enrichment recovery (103.5%±6.6% and 101.5%±10.4%). We identified a total of 86 glycopeptides derived from 53 glycoproteins with 94 -glycosylation sites from only 1 μL human serum. The O-T-D-COFs exhibited a good glycopeptide separation and enrichment potential, indicating that the COF material has promising application potential in glycoproteomics.
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http://dx.doi.org/10.3724/SP.J.1123.2021.02001DOI Listing
June 2021

Changes in physico-chemical characteristics and viable bacterial communities during fermentation of alfalfa silages inoculated with Lactobacillus plantarum.

World J Microbiol Biotechnol 2021 Jun 28;37(7):127. Epub 2021 Jun 28.

Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Zhaoaruda Road 306, Hohhot, 010018, People's Republic of China.

This study investigated the effect of inoculating Lactobacillus (L.) plantarum PS-8 in fermentation of alfalfa silages. We monitored the fermentation characteristics and bacterial population dynamics during the ensiling process. PacBio single molecule real time sequencing was combined with propidium monoazide (PMA) treatment to monitor the viable microbiota dynamics. We found that inoculating L. plantarum PS-8 may improve the silage quality by accelerating acidification, reducing the amounts of clostridia, coliform bacteria, molds and yeasts, elevating the protein and organic acid contents (except butyrate), and enhancing lactic acid bacteria (LAB) while suppressing harmful microorganisms. Some significant differential abundant taxa were found between the PMA-treated and non-treated microbiota. For example, the relative abundances of L. brevis, L. plantarum, and Pediococcus pentosaceus were significantly higher in the PMA-treated group than the non-PMA-treated group, suggesting obvious differences between the viable and non-viable microbiota. It would thus be necessary to distinguish between the viable and non-viable microbial communities to further understand their physiological contribution in silage fermentation. By tracking the dynamics of viable microbiota in relation with changes in the physico-chemical parameters, our study provided novel insights into the beneficial effects of inoculating L. plantarum PS-8 in silage fermentation and the physiological function of the viable bacterial communities.
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http://dx.doi.org/10.1007/s11274-021-03095-2DOI Listing
June 2021

Exploring the industrial potential of Lactobacillus delbrueckii ssp. bulgaricus by population genomics and genome-wide association study analysis.

J Dairy Sci 2021 Apr 2;104(4):4044-4055. Epub 2021 Mar 2.

Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China. Electronic address:

Lactobacillus delbrueckii ssp. bulgaricus is one of the most commonly used starter cultures for yogurt production. However, how its genetic background affects acid production capacity is unclear. This study investigated the industrial potential of L. delbrueckii ssp. bulgaricus using population genomics and GWAS analysis. To meet our goal, population genetics and functional genomics analyses were performed on 188 newly sequenced L. delbrueckii ssp. bulgaricus strains isolated from naturally fermented dairy products together with 19 genome sequences retrieved from the NCBI database. Four distinct clusters were identified, and they were correlated with the geographical sites where the samples were collected. The GWAS analysis about acidification fermentation results with sucrose-fortified reconstituted skim milk revealed a significant association between l-lactate dehydrogenase (lldD; Ldb2036) and the bacterial acid production rate. Our study has broadened the understanding of the population structure and genetic diversity of L. delbrueckii ssp. bulgaricus by identifying potential targets for further research, development, and use of lactic acid bacteria in the dairy industry.
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http://dx.doi.org/10.3168/jds.2020-19467DOI Listing
April 2021

Characterization and association of bacterial communities and nonvolatile components in spontaneously fermented cow milk at different geographical distances.

J Dairy Sci 2021 Mar 15;104(3):2594-2605. Epub 2021 Jan 15.

Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China. Electronic address:

In the ecosystem of spontaneously fermented cow milk, the characteristics and relationship of bacterial communities and nonvolatile components at different scales of geographical distances (provincial, county, and village levels) are unclear. Here, 25 sampling sites from Xin Jiang and Tibet, 2 provinces of China, were selected based on the distribution of spontaneously fermented cow milk and used for metagenomic and metabolomic analysis. At the provincial geographical distance, the same predominant species, Lactobacillus delbrueckii ssp. bulgaricus and Streptococcus thermophilus, were detected in Xin Jiang and Tibet. Further, the richness of the bacterial composition of samples from Tibet was higher than those from Xin Jiang; specifically, at the species level, 28 species were identified in Tibet samples but only 7 species in Xin Jiang samples. At the provincial geographical level, we detected significant differences in bacterial structure, shown in principal coordinate analysis plots, and significant differences (Simpson index) in bacterial diversity were also detected. However, at the county and village levels, no significant differences were detected in bacterial communities and diversity, but a difference in bacterial compositions was detectable. This indicates that bacterial communities and diversity of spontaneously fermented milk dissimilarity significantly increased with geographic distance. For the nonvolatile component profiles, the partial least squares discriminant analysis plot (RY > 0.5 and Q > 0.5 for the goodness-of-fit and predictive ability parameter, respectively) showed that samples from different geographical distances (provincial, county, and village) were all separated, which indicated that all the discriminations in nonvolatile components profiles were from different geographical distances. Investigating relationships between lactic acid bacteria and discriminatory nonvolatile components at the county level showed that 9 species were positively correlated with 16 discriminatory nonvolatile components, all species with low abundance rather than the predominant species L. delbrueckii ssp. bulgaricus and Strep. thermophilus, which indicates the importance of the selection of autochthonous nonpredominant bacteria.
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http://dx.doi.org/10.3168/jds.2020-19303DOI Listing
March 2021

The antagonistic effects and mechanisms of microRNA-26a action in hypertensive vascular remodelling.

Br J Pharmacol 2021 03 28;178(5):1037-1054. Epub 2021 Jan 28.

Department of Cardiology, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, P.R. China.

Background And Purpose: Hypertensive vascular remodelling is responsible for end-organ damage and is the result of increased extracellular matrix accumulation and excessive vascular smooth muscle cell (VSMC) proliferation. MicroRNA-26a (miR-26a), a non-coding small RNA, is involved in several cardiovascular diseases. We aimed to validate the effect and mechanisms of miR-26a in hypertensive vascular remodelling.

Experimental Approach: Male spontaneously hypertensive rats (SHRs) were injected intravenously with recombinant adeno-associated virus-miR-26a. Samples of thoracic aorta were examined histologically with H&E staining. In vitro, angiotensin II (AngII)-induced VSMCs cultured from thoracic aortae of female Sprague-Dawley rats, were transfected with miR-26a mimic or inhibitor. Western blots, qRT-PCR and immunohistological methods were used, along with chromatin-immunoprecipitation and luciferase reporter assays. Specific siRNAs were used to silence Smad production in VSMCs KEY RESULTS: Levels of miR-26a were lower in the thoracic aorta and plasma of SHRs than in WKY rats. Overexpression of miR-26a inhibited extracellular matrix deposition by targeting connective tissue growth factor (CTGF) and decreased VSMC proliferation by regulating the enhancer of zeste homologue 2 (EZH2)/p21 pathway both in vitro and in vivo. AngII-mediated Smad3 activation suppressed miR-26a expression, which in turn promoted Smad3 activation via targeted regulation of Smad4, leading to further down-regulation of miR-26a.

Conclusion And Implications: Our data show that AngII stimulated a Smads/miR-26a positive feedback loop, which further reduced expression of miR-26a, leading to collagen production and VSMC proliferation and consequently vascular remodelling. MiR-26a has an antagonistic effect on hypertensive vascular remodelling and can be a strategy for treating hypertensive vascular remodelling.
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http://dx.doi.org/10.1111/bph.15337DOI Listing
March 2021

Fermentation Characteristics of subsp. Isolated From Naturally Fermented Dairy Products and Screening of Potential Starter Isolates.

Front Microbiol 2020 4;11:1794. Epub 2020 Aug 4.

Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China.

It is well known that consumers are keen to try fermented milk products with different flavors and starter cultures are important in determining the resulting fermented dairy products. Here, we present the phenome of 227 subsp. isolates from traditionally fermented dairy products and the selection of potential starter strains. Large-scale phenotyping revealed significant technological diversity in fermentation characteristics amongst the isolates including variation in fermentation time, viscosity, water holding capacity (WHC) and free amino nitrogen (FAN) production. The 16 isolates with the best fermentation characteristics were compared, in a sensory evaluation, with the commercial starter Chr. Hansen R-704 as excellent fermentation characteristics to identify potential starter isolates and find the isolate which can product good flavors. From these, and from solid phase micro extraction (SPME) - gas chromatography (GC)-mass spectrometry (MS) analysis, we identified IMAU11823 and IMAU11919 as producing 3-methyl butanal and 3-methyl-2-butanone which contribute to the malt aroma. This study expands the characterization of subsp. phenotypic dataset and technological diversity and identified isolates with potential culture starter in the fermentation industry.
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http://dx.doi.org/10.3389/fmicb.2020.01794DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7438938PMC
August 2020

MicroRNA-26a Protects the Heart Against Hypertension-Induced Myocardial Fibrosis.

J Am Heart Assoc 2020 09 31;9(18):e017970. Epub 2020 Aug 31.

Department of Cardiology The Second Affiliated Hospital Xi'an Jiaotong University Xi'an Shaanxi People's Republic of China.

Background Hypertensive myocardial fibrosis (MF) is characterized by excessive deposition of extracellular matrix and cardiac fibroblast proliferation, which can lead to heart failure, malignant arrhythmia, and sudden death. In recent years, with the deepening of research, microRNAs have been found to have an important role in blood pressure control and maintaining normal ventricular structure and function. Methods and Results In this study, we first documented the downregulation of microRNA-26a (miR-26a) in the plasma and myocardium of spontaneously hypertensive rats; more importantly, miR-26a-deficient mice showed MF, whereas overexpression of miR-26a significantly prevented elevated blood pressure and inhibited MF in vivo and angiotensin II-induced fibrogenesis in cardiac fibroblasts by directly targeting connective tissue growth factor and Smad4. miR-26a inhibited cardiac fibroblast proliferation by the enhancer of zeste homolog 2/p21 pathway. Conclusions Our study identified a novel role for miR-26a in blood pressure control and hypertensive MF and provides a possible treatment strategy for miR-26a to alleviate and reverse hypertensive MF.
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http://dx.doi.org/10.1161/JAHA.120.017970DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7726969PMC
September 2020

Preparation of a novel monolith-based adsorbent for solid-phase microextraction of sulfonamides in complex samples prior to HPLC-MS/MS analysis.

Anal Chim Acta 2020 Jun 18;1118:9-17. Epub 2020 Apr 18.

Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen, 361005, PR China. Electronic address:

Effective extraction is an essential step in the sensitive and accurate analysis of sulfonamides (SAs) in complex samples. In this study, based on the chemical properties of SAs, a novel monolith-based adsorbent using 4-vinylbenzoic acid and 4-vinylphenylboronic acid as dual-functional monomers was tailored and employed as efficient extraction phase of solid-phase microextraction. Various characterized techniques were applied to investigate the structure and morphology of the obtained adsorbent. Due to the abundant functional groups, the synthetic adsorbent displayed satisfying extraction performance for target SAs through multiple interactions including ion-exchange, B-N coordination, π-π and hydrophobic interactions. Following elution with the desorption solution of methanol/formic acid (98.5/1.5, v/v), the extractive SAs were measured by HPLC-MS/MS. Under the optimized conditions, the proposed approach exhibited wide linear ranges (0.005-10.0 μg/L for most of analytes), low limits of detection (in the range of 0.31-2.3 ng/L) and good precision (RSDs were lower than 8.0%). In the analysis of target SAs in environment waters and honey samples, the recoveries at low, medium and high spiked concentrations were in the range of 83.5-119%, and the RSDs (n = 3) varied from 0.6% to 9.6%. Compared with existing approaches, the current method presents some merits such as high sensitivity, good reproducibility, low consumptions of sample and organic solvent.
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http://dx.doi.org/10.1016/j.aca.2020.04.035DOI Listing
June 2020

Facile fabrication of functional groups-rich sorbent for the efficient enrichment of aromatic N- and S-containing compounds in environmental waters.

Anal Chim Acta 2020 May 1;1113:36-42. Epub 2020 Apr 1.

State Key Laboratory of Marine Environmental Science, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China. Electronic address:

Extraction strategy is designed for the pretreatment of low contents of aromatic N- and S-containing compounds (ANSCs) in environmental waters prior to chromatographic analysis. To enrich studied ANSCs effectively, poly (9-vinylanthracene/4-vinylphenylboronic acid-co-ethylene dimethacrylate/divinylbenzene) polymeric monolithic sorbent were facilely fabricated using the one-step free radical polymerization. Various technologies were employed to investigate the structure and morphology of the resultant monolith. Combining with solid-phase microextraction format, the sorbent exhibited satisfying concentrated performance for ANSCs through multiply interactions under the optimized conditions. After desorption with eluent, the retained analytes were analyzed by HPLC. Results showed that the extraction efficiencies ranged from 51.6 to 93.2%. The linear ranges and limits of detection were 0.01-150 μg/L and 0.63-2.64 ng/L, respectively. Furthermore, the precisions were all below 10%. The introduced approach was productively practiced on three real water samples for simultaneous quantification of studied ANSCs, and the fortified recoveries ranged from 81.5 to 118%. All the results well evidenced that prepared sorbent can enrich ANSCs effectively and the introduced method is reliable alternative for routine analysis of ANSCs in environmental waters.
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http://dx.doi.org/10.1016/j.aca.2020.03.056DOI Listing
May 2020

Profiling of koumiss microbiota and organic acids and their effects on koumiss taste.

BMC Microbiol 2020 04 10;20(1):85. Epub 2020 Apr 10.

Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, People's Republic of China.

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 koumiss samples. The dominant bacterial species in koumiss were Lactobacillus helveticus, Lactobacillus kefiranofaciens, Lactococcus lactis, Lactococcus raffinolactis, and Citrobacter freundii. The main yeast species were Dekkera anomala, Kazachstania unispora, Meyerozyma caribbica, Pichia sp.BZ159, Kluyveromyces marxianus, and uncultured Guehomyces. The bacterial and yeast Shannon diversity of the Xilinhaote-urban group were higher than those of the Xilingol-rural group. The most dominant organic acids were lactic, acetic, tartaric, and malic acids. Lactic acid bacteria species were mostly responsible for the accumulation of those organic acids, although Kazachstania unispora, Dekkera anomala, and Meyerozyma caribbica may also have contributed. Redundancy analysis suggested that both bacteria and yeast respond to koumiss flavor, such as Lactobacillus helveticus and Dekkera anomala are associated with sourness, astringency, bitterness, and aftertaste, whereas Lactococcus lactis and Kazachstania unispora are associated with umami.

Conclusions: Our results suggest that differences were observed in koumiss microbiota of Xilinhaote-urban and Xilingol-rural samples. The biodiversity of the former was higher than the latter group. Positive or negative correlations between bacteria and yeast species and taste also were found.
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http://dx.doi.org/10.1186/s12866-020-01773-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7149844PMC
April 2020

sp. nov., a novel arsenic-resistant bacterium.

Int J Syst Evol Microbiol 2020 Apr 4;70(4):2580-2587. Epub 2020 Mar 4.

Northwest Hubei Research Institute of Traditional Fermented Food, College of Food Science and Technology, Hubei University of Arts and Science, Xiangyang, Hubei, PR China.

A lactic acid bacterial strain, HBUAS57009, isolated from traditionally fermented food (Zha-Chili) in China, was characterized to clarify its taxonomic status using a polyphasic approach. Strain HBUAS57009 was phylogenetically closely related to DCY50, 218-6, 112-3, TUM BP 140423000-2250, 218-10 and THK-V8 with sequence similarities of 98.6-99.3 %. The genome-to-genome distance and average nucleotide identity values between the genomes of strain HBUAS57009 and type strains of closely related species were less than 32.0 and 86.0 %, respectively; this is below the threshold for species boundaries. The major cellular fatty acids (>10 %) were C, C ω9 and iso-C. The G+C content of the genomic DNA of strain HBUAS57009 was 47.8 mol%. Examination of the functional categories of the genome revealed that strain HBUAS57009 could perform both homolactic and heterolactic fermentation processes to produce lactic acid via complete glycolysis and the pentose phosphate pathway. The putative biosynthesis pathway of butane-2,3-diol and acetoin, two important flavour compounds in the food industry, were identified using kegg mapper analysis. Based on its genotypic and phenotypic features, strain HBUAS57009 (=GDMCC 1.1664=KACC 21424) is designated as the type strain of a novel species, for which the name sp. nov. is proposed.
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http://dx.doi.org/10.1099/ijsem.0.004072DOI Listing
April 2020

Profiling of the viable bacterial and fungal microbiota in fermented feeds using single-molecule real-time sequencing.

J Anim Sci 2020 Feb;98(2)

Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China.

Fermented concentrated feed has been widely recognized as an ideal feed in the animal industry. In this study, we used a powerful method, coupling propidium monoazide (PMA) pretreatment with single-molecule real-time (SMRT) sequencing technology to compare the bacterial and fungal composition of feeds before and after fermentation with four added lactic acid bacteria (LAB) inoculants (one Lactobacillus casei strain and three L. plantarum strains). Five feed samples consisting of corn, soybean meal, and wheat bran were fermented with LAB additives for 3 d. Following anaerobic fermentation, the pH rapidly decreased, and the mean numbers of LAB increased from 106 to 109 colony-forming units (cfu)/g fresh matter. SMRT sequencing results showed that the abundance and diversity of bacteria and fungi in the feed were significantly higher before fermentation than after fermentation. Fifteen bacterial species and eight fungal genera were significantly altered following fermentation, and L. plantarum was the dominant species (relative abundance 88.94%) in the post-fermentation group. PMA treatment revealed that the bacteria Bacillus cereus, B. circulans, Alkaliphilus oremlandii, Cronobacter sakazakii, Paenibacillus barcinonensis, and P. amylolyticus (relative abundance >1%) were viable in the raw feed. After fermentation, their relative abundances decreased sharply to <0.2%; however, viable L. plantarum was still the dominant species post fermentation. We inferred that our LAB additives grew rapidly and inhibited harmful microorganisms and further improved feed quality. In addition, coupling PMA treatment with the Pacific Biosciences SMRT sequencing technology was a powerful tool for providing accurate live microbiota profiling data in this study.
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http://dx.doi.org/10.1093/jas/skaa029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7036599PMC
February 2020
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