Infant intestinal microbiome is closely linked with health and risk of disease. Bifidobacterium are important components of the infant gut and are known to confer various health effects on the host. However, few studi...Infant intestinal microbiome is closely linked with health and risk of disease. Bifidobacterium are important components of the infant gut and are known to confer various health effects on the host. However, few studies have described the precise composition and dynamics of early infant gut bifidobacterial communities. Thus, this was a pilot study aiming to describe the developmental trajectories and temporal dynamics of bifidobacterial communities in infants before 6 months of age. A total of 28 fecal samples from 4 infants(GF, ZZ, QM, TN, respectively)were collected and analyzed after 5, 15, 30, 60, 90, 120, 150, and 180 days of birth by a bifidobacteria-target method(based on single-molecule real-time sequencing of partial bifidobacterial rpsK genes)in conjunction with droplet digital polymerase chain reaction(ddPCR). The infant fecal microbiota comprised a total of 11 bifidobacterial species, including 4 major species, i.e., B. dentium(37.35%), B. catenulatum(32.04%), B. breve(22.24%), and B. animalis(8.02%). The infant microbiota showed highly individualized developmental trajectories. The leading species for GF was B. catenulatum, with a relatively stable developmental trajectory. In ZZ, B. breve was enriched, and the developmental trajectory was rather fluctuating. The most abundant species for QM and TN was B. dentium. The developmental trajectory of B. dentium in QM showed a trend of gradual decrease, whereas an opposite trend was seen in samples of TN. The results of ddPCR confirmed large variations in quantities of bifidobacteria between infants and suggested discordances in temporal dynamics of bifidobacterial communities during the first half year of infancy. In conclusion, our results suggested that the early infant gut bifidobacterial microbiota was highly complex and temporal dynamics, with individualized developmental trajectories, which should be considered in future research of infant gut microbiota.展开更多
Panax quinquefolium is one of the most common medicinal plants worldwide.Ginsenosides are the major pharmaceutical components in P.quinquefolium.The biosynthesis of ginsenosides in different tissues of P.quinquefolium...Panax quinquefolium is one of the most common medicinal plants worldwide.Ginsenosides are the major pharmaceutical components in P.quinquefolium.The biosynthesis of ginsenosides in different tissues of P.quinquefolium remained largely unknown.In the current study,an integrative method of transcriptome and metabolome analysis was used to elucidate the ginsenosides biosynthesis pathways in different tissues of P.quinquefolium.Herein,22 ginsenosides in roots,leaves,and flower buds showed uneven distribution patterns.A comprehensive P.quinquefolium transcriptome was generated through single molecular real-time(SMRT)and second-generation sequencing(NGS)technologies,which revealed the ginsenoside pathway genes and UDP-glycosyltransferases(UGT)family genes explicitly expressed in roots,leaves,and flower buds.The weighted gene co-expression network analysis(WGCNA)of ginsenoside biosynthesis genes,UGT genes and ginsenoside contents indicated that three UGT genes were positively correlated to pseudoginsenoside F11,notoginsenoside R1,notoginsenoside R2 and pseudoginsenoside RT5.These results provide insights into ginsenoside biosynthesis in different tissues ofP.quinquefolium.展开更多
Chinese cabbage is an economically important Brassica vegetable worldwide, and clubroot, which is caused by the soilborne protist plant pathogen Plasmodiophora brassicae is regarded as a destructive disease to Brassic...Chinese cabbage is an economically important Brassica vegetable worldwide, and clubroot, which is caused by the soilborne protist plant pathogen Plasmodiophora brassicae is regarded as a destructive disease to Brassica crops. Previous studies on the gene transcripts related to Chinese cabbage resistance to clubroot mainly employed RNA-seq technology,although it cannot provide accurate transcript assembly and structural information. In this study, PacBio RS II SMRT sequencing was used to generate full-length transcriptomes of mixed roots at 0, 2, 5, 8, 13, and 22 days after P. brassicae infection in the clubroot-resistant line DH40R. Overall, 39 376 high-quality isoforms and 26 270 open reading frames(ORFs) were identified from the SMRT sequencing data. Additionally, 426 annotated long noncoding RNAs(lncRNAs),56 transcription factor(TF) families, 1 883 genes with poly(A) sites and 1 691 alternative splicing(AS) events were identified. Furthermore, 1 201 of the genes had at least one AS event in DH40R. A comparison with RNA-seq data revealed six differentially expressed AS genes(one for disease resistance and five for defensive response) that are potentially involved in P. brassicae resistance. The results of this study provide valuable resources for basic research on clubroot resistance in Chinese cabbage.展开更多
Sulfate-reducing bacteria(SRB)are ubiquitous anaerobic microorganisms that play signifi cant roles in the global biogeochemical cycle.Coastal wetlands,one of the major habitats of SRB,exhibit high sulfate-reducing act...Sulfate-reducing bacteria(SRB)are ubiquitous anaerobic microorganisms that play signifi cant roles in the global biogeochemical cycle.Coastal wetlands,one of the major habitats of SRB,exhibit high sulfate-reducing activity and thus play signifi cant roles in organic carbon remineralization,benthic geochemical action,and plant-microbe interactions.Recent studies have provided credible evidence that the functional rather than the taxonomic composition of microbes responds more closely to environmental factors.Therefore,in this study,functional gene prediction based on PacBio single molecular real-time sequencing of 16S rDNA was applied to determine the sulfate-reducing and organic substrate-decomposing activities of SRB in the rhizospheres of two typical coastal wetland plants in North and South China:Zostera japonica and Scirpus mariqueter.To this end,some physicochemical characteristics of the sediments as well as the phylogenetic structure,community composition,diversity,and proportions of several functional genes of the SRB in the two plant rhizospheres were analyzed.The Z.japonic a meadow had a higher dissimilatory sulfate reduction capability than the S.mariqueter-comprising saltmarsh,owing to its larger proportion of SRB in the microbial community,larger proportions of functional genes involved in dissimilatory sulfate reduction,and the stronger ability of the SRB to degrade organic substrates completely.This study confi rmed the feasibility of applying microbial community function prediction in research on the metabolic features of SRB,which will be helpful for gaining new knowledge of the biogeochemical and ecological roles of these bacteria in coastal wetlands.展开更多
Cobetia marina is a model proteobacteria in researches on marine biofouling. Its taxonomic nomenclature has been revised many times over the past few decades. ~To better understand the role of the surface-associated l...Cobetia marina is a model proteobacteria in researches on marine biofouling. Its taxonomic nomenclature has been revised many times over the past few decades. ~To better understand the role of the surface-associated lifestyle of C. marina and the phylogeny of the family Halomonadaceae, we sequenced the entire genome of C. marina JCM 21022 ~T using single molecule real-time sequencing technology(SMR^T) and performed comparative genomics and phylogenomics analyses. ~The circular chromosome was 4 176 300 bp with an average GC content of 62.44% and contained 3 611 predicted coding sequences, 72 t RNA genes, and 21 r RNA genes. ~The C. marina JCM 21022 ~T genome contained a set of crucial genes involved in surface colonization processes. ~The comparative genome analysis indicated the significant diff erences between C. marina JCM 21022 ~T and Cobetia amphilecti KMM 296(formerly named C. marina KMM 296) resulted from sequence insertions or deletions and chromosomal recombination. Despite these diff erences, pan and core genome analysis showed similar gene functions between the two strains. ~The phylogenomic study of the family Halomonadaceae is reported here for the first time. We found that the relationships were well resolved among every genera tested, including Chromohalobacter, Halomonas, Cobetia, Kushneria, Zymobacter, and Halotalea.展开更多
Portunus trituberculatus is an ide al model for elucidating crustacean genetic networks.Here we combined single molecule real-time(SMRT)sequencing and Illumina RNA-seq to characterize the coding genes,non-coding RNAs ...Portunus trituberculatus is an ide al model for elucidating crustacean genetic networks.Here we combined single molecule real-time(SMRT)sequencing and Illumina RNA-seq to characterize the coding genes,non-coding RNAs and pseudogenes and further to improve the genome annotation information of P.tritub erculatus.In this study,we assembled 9694 non-redundancy full-length transcripts,and 658737307-bp repetitive sequences were identified in the P.trituberculatus full-length transcriptome.We also predicted the P.tritub erculatus genome structure based on full-length transcripts,including 18602 genes,28686 non-coding RNAs,1407 pseudogenes,740 motif,and 26434 domain.Meanwhile,14460,10211,5412,7314,and 14448 genes had significant matches with sequences in the NR,KOG,GO,KEGG,and TrEMBL database,respectively.Overall,our work firstly provided the long-read transcriptome and we believed that these data are very necessary to improve the annotation information of P.trituberculatus genome structure,and useful information for the future studies on evolution and physiological regulation of P.trituberculatus.展开更多
Global concerns have been paid to the potential hazard of traditional herbal medicinal products(THMPs). Substandard and counterfeit THMPs, including traditional Chinese patent medicine, health foods, dietary supplemen...Global concerns have been paid to the potential hazard of traditional herbal medicinal products(THMPs). Substandard and counterfeit THMPs, including traditional Chinese patent medicine, health foods, dietary supplements, etc. are potential threats to public health. Recent marketplace studies using DNA barcoding have determined that the current quality control methods are not sufficient for ensuring the presence of authentic herbal ingredients and detection of contaminants/adulterants. An efficient biomonitoring method for THMPs is of great needed. Herein, metabarcoding and single-molecule, realtime(SMRT) sequencing were used to detect the multiple ingredients in Jiuwei Qianghuo Wan(JWQHW), a classical herbal prescription widely used in China for the last 800 years. Reference experimental mixtures and commercial JWQHW products from the marketplace were used to confirm the method. Successful SMRT sequencing results recovered 5416 and 4342 circular-consensus sequencing(CCS) reads belonging to the ITS2 and psb A-trn H regions. The results suggest that with the combination of metabarcoding and SMRT sequencing, it is repeatable, reliable, and sensitive enough to detect species in the THMPs, and the error in SMRT sequencing did not affect the ability to identify multiple prescribed species and several adulterants/contaminants. It has the potential for becoming a valuable tool for the biomonitoring of multi-ingredient THMPs.展开更多
Conventional filling therapy fails to fundamentally reduce oral cariogenic bacteria.Thus,oral microbiota follow-up intervention after filling would be necessary for improving dental caries prognosis.We recruited 9 car...Conventional filling therapy fails to fundamentally reduce oral cariogenic bacteria.Thus,oral microbiota follow-up intervention after filling would be necessary for improving dental caries prognosis.We recruited 9 caries-free individuals,and 89 dental caries subjects(5 dropouts).Eighty-nine patients were randomized into three groups:caries(n=8;no treatment),control(n=40;filling),and postbiotics(n=41;filling and 14-day Probio-Eco®intervention).Salivary samples were collected at 0 day(after filling)and 14 days.Our results showed that the diversity of dental caries oral microbiota was significantly increased compared with healthy subjects,and filling could restore a healthier oral microbiota partially and temporarily.Thepostbiotics intervention keeps a low alpha-diversity.Co-occurrence network analysis showed that a more stable oral microbiota structure after postbiotics intervention.Taxonomic and functional annotation of the microbiota revealed that postbiotics co-treatment significantly:increased the relative abundance of Pseudomonas and P.reactans,decreased the relative abundance of Prevotella shahii,and enriched the energy metabolism-related pathways.BugBase-predicted phenotypes inferred to an oral microbiota with decreased potential pathogenic bacteria and increased oxidative stress-tolerant bacteria after postbiotics intervention.Collectively,it suggested that postbiotics co-treatment could be a promising strategy that restores the oral microecological balance for dental caries.展开更多
Sepsis-induced liver injury(SILI)is an important cause of septicemia deaths.BaWeiBaiDuSan(BWBDS)was extracted from a formula of Panax ginseng C.A.Meyer,Lilium brownie F.E.Brown ex Miellez var.viridulum Baker,Polygonat...Sepsis-induced liver injury(SILI)is an important cause of septicemia deaths.BaWeiBaiDuSan(BWBDS)was extracted from a formula of Panax ginseng C.A.Meyer,Lilium brownie F.E.Brown ex Miellez var.viridulum Baker,Polygonatum sibiricum Delar.ex Redoute,Lonicera japonica Thunb.,Hippophae rhamnoides Linn.,Amygdalus Communis Vas,Platycodon grandiflorus(Jacq.)A.DC.,and Cortex Phelloderdri.Herein,we investigated whether the BWBDS treatment could reverse SILI by the mechanism of modulating gut microbiota.BWBDS protected mice against SILI,which was associated with promoting macrophage anti-inflammatory activity and enhancing intestinal integrity.BWBDS selectively promoted the growth of Lactobacillus johnsonii(L.johnsonii)in cecal ligation and puncture treated mice.Fecal microbiota transplantation treatment indicated that gut bacteria correlated with sepsis and was required for BWBDS anti-sepsis effects.Notably,L.johnsonii significantly reduced SILI by promoting macrophage anti-inflammatory activity,increasing interleukin-10+M2 macrophage production and enhancing intestinal integrity.Furthermore,heat inactivation L.johnsonii(HI-L.johnsonii)treatment promoted macrophage anti-inflammatory activity and alleviated SILI.Our findings revealed BWBDS and gut microbiota L.johnsonii as novel prebiotic and probiotic that may be used to treat SILI.The potential underlying mechanism was at least in part,via L.johnsonii-dependent immune regulation and interleukin-10+M2 macrophage production.展开更多
The gut microbiota of Mongolian hosts has distinctive characteristics due to their meat- and dairyoriented daily diets and unique genotype.The aim of the present study was to investigate the effect of switching from t...The gut microbiota of Mongolian hosts has distinctive characteristics due to their meat- and dairyoriented 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 the host gut microbiota within 3 weeks.Our study took the advantage of the long sequence reads produced by the Pac Bio single molecule real-time sequencing technology to enable the profiling of subjects' gut microbiota communities along the diet intervention to the species precision.We found that the bacterial richness and diversity decreased apparently along the diet intervention.During the diet intervention,the gut microbiota composition displayed no significant difference at phylum level(with major phyla of Firmicutes,Bacteroidetes,Tenericutes and Proteobacteria).The relative abundances of some genera such as Bacteroidetes,Faecalibacterium,Roseburia,Alistipes,Streptococcus,and Oscillospira were significantly altered after the diet switching started.Notably,significant changes were also observed in the proportions of the species Bacteroides dorei,Bacteroides fragilis,Bacteroides thetaiotaomicron,Ruminococcus albus,Ruminococcus faecis,Roseburia faecis and Eubacterium ventriosum.These results have demonstrated that diet and host gut microbiota is closely linked.展开更多
基金supported by the National Natural Science Foundation of China (31972083)the Natural Science Foundation of Inner Mongolia Autonomous Region (2020ZD12)+2 种基金the Inner Mongolia Science and Technology Major Projects (2021ZD0014)the Inner Mongolia Science & Technology Planning Project (2022YFSJ0017)China Agriculture Research System of MOF and MARA。
文摘Infant intestinal microbiome is closely linked with health and risk of disease. Bifidobacterium are important components of the infant gut and are known to confer various health effects on the host. However, few studies have described the precise composition and dynamics of early infant gut bifidobacterial communities. Thus, this was a pilot study aiming to describe the developmental trajectories and temporal dynamics of bifidobacterial communities in infants before 6 months of age. A total of 28 fecal samples from 4 infants(GF, ZZ, QM, TN, respectively)were collected and analyzed after 5, 15, 30, 60, 90, 120, 150, and 180 days of birth by a bifidobacteria-target method(based on single-molecule real-time sequencing of partial bifidobacterial rpsK genes)in conjunction with droplet digital polymerase chain reaction(ddPCR). The infant fecal microbiota comprised a total of 11 bifidobacterial species, including 4 major species, i.e., B. dentium(37.35%), B. catenulatum(32.04%), B. breve(22.24%), and B. animalis(8.02%). The infant microbiota showed highly individualized developmental trajectories. The leading species for GF was B. catenulatum, with a relatively stable developmental trajectory. In ZZ, B. breve was enriched, and the developmental trajectory was rather fluctuating. The most abundant species for QM and TN was B. dentium. The developmental trajectory of B. dentium in QM showed a trend of gradual decrease, whereas an opposite trend was seen in samples of TN. The results of ddPCR confirmed large variations in quantities of bifidobacteria between infants and suggested discordances in temporal dynamics of bifidobacterial communities during the first half year of infancy. In conclusion, our results suggested that the early infant gut bifidobacterial microbiota was highly complex and temporal dynamics, with individualized developmental trajectories, which should be considered in future research of infant gut microbiota.
基金supported by the National Natural Science Foundation of China(No.81703635)the National Key R&D Program of China(No.2021YFD1600900)the Jilin Province Science and Technology Development Project(No.20210101190JC,20200504001YY)。
文摘Panax quinquefolium is one of the most common medicinal plants worldwide.Ginsenosides are the major pharmaceutical components in P.quinquefolium.The biosynthesis of ginsenosides in different tissues of P.quinquefolium remained largely unknown.In the current study,an integrative method of transcriptome and metabolome analysis was used to elucidate the ginsenosides biosynthesis pathways in different tissues of P.quinquefolium.Herein,22 ginsenosides in roots,leaves,and flower buds showed uneven distribution patterns.A comprehensive P.quinquefolium transcriptome was generated through single molecular real-time(SMRT)and second-generation sequencing(NGS)technologies,which revealed the ginsenoside pathway genes and UDP-glycosyltransferases(UGT)family genes explicitly expressed in roots,leaves,and flower buds.The weighted gene co-expression network analysis(WGCNA)of ginsenoside biosynthesis genes,UGT genes and ginsenoside contents indicated that three UGT genes were positively correlated to pseudoginsenoside F11,notoginsenoside R1,notoginsenoside R2 and pseudoginsenoside RT5.These results provide insights into ginsenoside biosynthesis in different tissues ofP.quinquefolium.
基金supported by the National Natural Science Foundation of China (31872945 and 31801874)the earmarked fund for China Agricultural Research System (CARS-23-G15)+1 种基金the Funds for Distinguished Young Scientists from Henan Academy of Agricultural Sciences, China (2021JQ03)the Innovation Team of Henan Academy of Agricultural Sciences, China (2021TD06)。
文摘Chinese cabbage is an economically important Brassica vegetable worldwide, and clubroot, which is caused by the soilborne protist plant pathogen Plasmodiophora brassicae is regarded as a destructive disease to Brassica crops. Previous studies on the gene transcripts related to Chinese cabbage resistance to clubroot mainly employed RNA-seq technology,although it cannot provide accurate transcript assembly and structural information. In this study, PacBio RS II SMRT sequencing was used to generate full-length transcriptomes of mixed roots at 0, 2, 5, 8, 13, and 22 days after P. brassicae infection in the clubroot-resistant line DH40R. Overall, 39 376 high-quality isoforms and 26 270 open reading frames(ORFs) were identified from the SMRT sequencing data. Additionally, 426 annotated long noncoding RNAs(lncRNAs),56 transcription factor(TF) families, 1 883 genes with poly(A) sites and 1 691 alternative splicing(AS) events were identified. Furthermore, 1 201 of the genes had at least one AS event in DH40R. A comparison with RNA-seq data revealed six differentially expressed AS genes(one for disease resistance and five for defensive response) that are potentially involved in P. brassicae resistance. The results of this study provide valuable resources for basic research on clubroot resistance in Chinese cabbage.
基金Supported by the Scientifi c Research Fund of the Second Institute of Oceanography,Ministry of Natural Resources(MNR)(Nos.JB1906,JG1616,JG1910)the Zhejiang Qingshan Lake Innovation Platform for Marine Science and Technology(No.2017E80001)+4 种基金the Key Projects of Philosophy and Social Sciences Research,Ministry of Education(No.18JZD059)the National Key Technology Research and Development Program of the Ministry of Science and Technology of the China(No.2015BAD08B01)the State Key Laboratory of Satellite Ocean Environment Dynamics(No.SOEDZZ1902)the National Natural Science Foundation of China(No.41806136)the Project of Long Term Observation and Research Plan in the Changjiang Estuary and the Adjacent East China Sea(LORCE,14282)。
文摘Sulfate-reducing bacteria(SRB)are ubiquitous anaerobic microorganisms that play signifi cant roles in the global biogeochemical cycle.Coastal wetlands,one of the major habitats of SRB,exhibit high sulfate-reducing activity and thus play signifi cant roles in organic carbon remineralization,benthic geochemical action,and plant-microbe interactions.Recent studies have provided credible evidence that the functional rather than the taxonomic composition of microbes responds more closely to environmental factors.Therefore,in this study,functional gene prediction based on PacBio single molecular real-time sequencing of 16S rDNA was applied to determine the sulfate-reducing and organic substrate-decomposing activities of SRB in the rhizospheres of two typical coastal wetland plants in North and South China:Zostera japonica and Scirpus mariqueter.To this end,some physicochemical characteristics of the sediments as well as the phylogenetic structure,community composition,diversity,and proportions of several functional genes of the SRB in the two plant rhizospheres were analyzed.The Z.japonic a meadow had a higher dissimilatory sulfate reduction capability than the S.mariqueter-comprising saltmarsh,owing to its larger proportion of SRB in the microbial community,larger proportions of functional genes involved in dissimilatory sulfate reduction,and the stronger ability of the SRB to degrade organic substrates completely.This study confi rmed the feasibility of applying microbial community function prediction in research on the metabolic features of SRB,which will be helpful for gaining new knowledge of the biogeochemical and ecological roles of these bacteria in coastal wetlands.
基金Supported by the National Natural Science Foundation of China(Nos.41006082,31372517)
文摘Cobetia marina is a model proteobacteria in researches on marine biofouling. Its taxonomic nomenclature has been revised many times over the past few decades. ~To better understand the role of the surface-associated lifestyle of C. marina and the phylogeny of the family Halomonadaceae, we sequenced the entire genome of C. marina JCM 21022 ~T using single molecule real-time sequencing technology(SMR^T) and performed comparative genomics and phylogenomics analyses. ~The circular chromosome was 4 176 300 bp with an average GC content of 62.44% and contained 3 611 predicted coding sequences, 72 t RNA genes, and 21 r RNA genes. ~The C. marina JCM 21022 ~T genome contained a set of crucial genes involved in surface colonization processes. ~The comparative genome analysis indicated the significant diff erences between C. marina JCM 21022 ~T and Cobetia amphilecti KMM 296(formerly named C. marina KMM 296) resulted from sequence insertions or deletions and chromosomal recombination. Despite these diff erences, pan and core genome analysis showed similar gene functions between the two strains. ~The phylogenomic study of the family Halomonadaceae is reported here for the first time. We found that the relationships were well resolved among every genera tested, including Chromohalobacter, Halomonas, Cobetia, Kushneria, Zymobacter, and Halotalea.
基金Supported by the National Key Research and Development Program of China(No.2017YFA0604904)the Zhejiang Provincial Natural Science Foundation of China(No.LR21D060003)。
文摘Portunus trituberculatus is an ide al model for elucidating crustacean genetic networks.Here we combined single molecule real-time(SMRT)sequencing and Illumina RNA-seq to characterize the coding genes,non-coding RNAs and pseudogenes and further to improve the genome annotation information of P.tritub erculatus.In this study,we assembled 9694 non-redundancy full-length transcripts,and 658737307-bp repetitive sequences were identified in the P.trituberculatus full-length transcriptome.We also predicted the P.tritub erculatus genome structure based on full-length transcripts,including 18602 genes,28686 non-coding RNAs,1407 pseudogenes,740 motif,and 26434 domain.Meanwhile,14460,10211,5412,7314,and 14448 genes had significant matches with sequences in the NR,KOG,GO,KEGG,and TrEMBL database,respectively.Overall,our work firstly provided the long-read transcriptome and we believed that these data are very necessary to improve the annotation information of P.trituberculatus genome structure,and useful information for the future studies on evolution and physiological regulation of P.trituberculatus.
基金supported by the National Natural Science Foundation of China (Grant No. 81373922)Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences (Grant No. CIFMS, 2016-I2M-3–016)
文摘Global concerns have been paid to the potential hazard of traditional herbal medicinal products(THMPs). Substandard and counterfeit THMPs, including traditional Chinese patent medicine, health foods, dietary supplements, etc. are potential threats to public health. Recent marketplace studies using DNA barcoding have determined that the current quality control methods are not sufficient for ensuring the presence of authentic herbal ingredients and detection of contaminants/adulterants. An efficient biomonitoring method for THMPs is of great needed. Herein, metabarcoding and single-molecule, realtime(SMRT) sequencing were used to detect the multiple ingredients in Jiuwei Qianghuo Wan(JWQHW), a classical herbal prescription widely used in China for the last 800 years. Reference experimental mixtures and commercial JWQHW products from the marketplace were used to confirm the method. Successful SMRT sequencing results recovered 5416 and 4342 circular-consensus sequencing(CCS) reads belonging to the ITS2 and psb A-trn H regions. The results suggest that with the combination of metabarcoding and SMRT sequencing, it is repeatable, reliable, and sensitive enough to detect species in the THMPs, and the error in SMRT sequencing did not affect the ability to identify multiple prescribed species and several adulterants/contaminants. It has the potential for becoming a valuable tool for the biomonitoring of multi-ingredient THMPs.
基金approved by the Medical Ethics Committee of Affiliated Stomatological Hospital of Nanchang University(2019015).
文摘Conventional filling therapy fails to fundamentally reduce oral cariogenic bacteria.Thus,oral microbiota follow-up intervention after filling would be necessary for improving dental caries prognosis.We recruited 9 caries-free individuals,and 89 dental caries subjects(5 dropouts).Eighty-nine patients were randomized into three groups:caries(n=8;no treatment),control(n=40;filling),and postbiotics(n=41;filling and 14-day Probio-Eco®intervention).Salivary samples were collected at 0 day(after filling)and 14 days.Our results showed that the diversity of dental caries oral microbiota was significantly increased compared with healthy subjects,and filling could restore a healthier oral microbiota partially and temporarily.Thepostbiotics intervention keeps a low alpha-diversity.Co-occurrence network analysis showed that a more stable oral microbiota structure after postbiotics intervention.Taxonomic and functional annotation of the microbiota revealed that postbiotics co-treatment significantly:increased the relative abundance of Pseudomonas and P.reactans,decreased the relative abundance of Prevotella shahii,and enriched the energy metabolism-related pathways.BugBase-predicted phenotypes inferred to an oral microbiota with decreased potential pathogenic bacteria and increased oxidative stress-tolerant bacteria after postbiotics intervention.Collectively,it suggested that postbiotics co-treatment could be a promising strategy that restores the oral microecological balance for dental caries.
基金funded by regular grants and joint grant(File No.0096/2018/A3,0111/2020/A3 and 0056/2020/AMJ)Dr.Neher’s Biophysics Laboratory for Innovative Drug Discovery(File No.001/2020/ALC)+4 种基金supported by the Macao Science and Technology Development Fundsupported by 2020 Young Qihuang Scholar funded by the National Administration of Traditional Chinese Medicinesupported by National Natural Science Foundation of China(82025036)supported by the Start-up Research Grant of University of Macao(SRG2022-00020-FHS,China)the Faculty of Health Science,University of Macao(Macao,China).
文摘Sepsis-induced liver injury(SILI)is an important cause of septicemia deaths.BaWeiBaiDuSan(BWBDS)was extracted from a formula of Panax ginseng C.A.Meyer,Lilium brownie F.E.Brown ex Miellez var.viridulum Baker,Polygonatum sibiricum Delar.ex Redoute,Lonicera japonica Thunb.,Hippophae rhamnoides Linn.,Amygdalus Communis Vas,Platycodon grandiflorus(Jacq.)A.DC.,and Cortex Phelloderdri.Herein,we investigated whether the BWBDS treatment could reverse SILI by the mechanism of modulating gut microbiota.BWBDS protected mice against SILI,which was associated with promoting macrophage anti-inflammatory activity and enhancing intestinal integrity.BWBDS selectively promoted the growth of Lactobacillus johnsonii(L.johnsonii)in cecal ligation and puncture treated mice.Fecal microbiota transplantation treatment indicated that gut bacteria correlated with sepsis and was required for BWBDS anti-sepsis effects.Notably,L.johnsonii significantly reduced SILI by promoting macrophage anti-inflammatory activity,increasing interleukin-10+M2 macrophage production and enhancing intestinal integrity.Furthermore,heat inactivation L.johnsonii(HI-L.johnsonii)treatment promoted macrophage anti-inflammatory activity and alleviated SILI.Our findings revealed BWBDS and gut microbiota L.johnsonii as novel prebiotic and probiotic that may be used to treat SILI.The potential underlying mechanism was at least in part,via L.johnsonii-dependent immune regulation and interleukin-10+M2 macrophage production.
文摘The gut microbiota of Mongolian hosts has distinctive characteristics due to their meat- and dairyoriented 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 the host gut microbiota within 3 weeks.Our study took the advantage of the long sequence reads produced by the Pac Bio single molecule real-time sequencing technology to enable the profiling of subjects' gut microbiota communities along the diet intervention to the species precision.We found that the bacterial richness and diversity decreased apparently along the diet intervention.During the diet intervention,the gut microbiota composition displayed no significant difference at phylum level(with major phyla of Firmicutes,Bacteroidetes,Tenericutes and Proteobacteria).The relative abundances of some genera such as Bacteroidetes,Faecalibacterium,Roseburia,Alistipes,Streptococcus,and Oscillospira were significantly altered after the diet switching started.Notably,significant changes were also observed in the proportions of the species Bacteroides dorei,Bacteroides fragilis,Bacteroides thetaiotaomicron,Ruminococcus albus,Ruminococcus faecis,Roseburia faecis and Eubacterium ventriosum.These results have demonstrated that diet and host gut microbiota is closely linked.