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Determining the protective effects of Ma-Mu-Ran Antidiarrheal Capsules against acute Dss-induced enteritis using 16s rrna gene sequencing and fecal metabolomics

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Chinese Journal of Natural Medicines 2022年第5期20卷 364-377页

作者： ZHENG si-Li ZHANG Dong-Ning DU AN Yan-Fen HUANG Fang HAN Lin-Tao MO Guo-Yan Pharmacy Faculty Hubei University of Chinese MedicineWuhan 430065China College of Basic Medical sciences Hubei University of Chinese MedicineWuhan 430065China Xinjiang Uygur Pharmaceutical Co. Ltd.UrumqiXinjiang 830026China

Ma-Mu-Ran Antidiarrheal Capsules(MMRAC)is traditional Chinese medicine that has been used to treat diarrhea caused by acute enteritis(AE)and bacillary dysentery in Xinjiang(China)for many ***,the potential therapeutic mechanism of MMRAC for AE and its regulatory mechanism on host metabolism is *** study used fecal metabolomics profiling with GC/Ms and 16s rrna gene sequencing analysis to explore the potential regulatory mechanisms of MMRAC on a dextran sulfate sodium salt(Dss)-induced mouse model of *** metabolomics-based analyses were performed to detect the differentially expressed metabolites and metabolic *** 16s rrna gene sequencing analysis was used to assess the altered gut microbes at the genus level and for functional ***,Pearson correlation analysis was used to integrate differentially expressed metabolites and altered bacterial *** results revealed that six intestinal bacteria and seven metabolites mediated metabolic disorders(i.e.,metabolism of amino acid,carbohydrate,cofactors and vitamins,and lipid)in AE ***,ten altered microbes mediated the differential expression of eight metabolites and regulated these metabolisms after MMRAC ***,these findings demonstrate that AE is associated with metabolic disorders and microbial ***,we present that MMRAC exerts protective effects against AE by improving host metabolism through the intestinal flora.

关键词： Acute enteritis Ma-Mu-Ran Antidiarrheal Capsules 16s rrna sequencing Fecal metabolomics Gut microbiota

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Identification of Bacterial Fish Pathogens in Brazil by Direct Colony PCR and 16s rrna Gene sequencing

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Advances in Microbiology 2015年第6期5卷 409-424页

作者： F.A.sebastiao L.R.Furlan D.T.Hashimoto F.Pilarski Aquaculture Center of sao Paulo state University—CAUNEsP Universidade Estadual PaulistaJaboticabalBrazil

Intensive fish farming systems in Brazil have increased the disease incidence, mainly of bacterial origin, due to higher stocking density, high organic matter levels and poor quality of the aquatic environment that causes high mortality rates during outbreaks. The identification of pathogenic species using a fast and reliable method of diagnosis is essential for successful epidemiological studies and disease control. The present study evaluated the use of direct colony PCR in combination with 16s rrna gene sequencing to diagnose fish bacterial diseases, with the goal of reducing the costs and time necessary for bacterial identification. The method was successful for all 178 isolates tested and produced bands with the same intensity as the standard PCR performed using pure DNA. In conclusion, the genetics methods allowed detecting the most common and important pathogens in Aquaculture, including 12 species of occurrence in Brazilian fish farms. The results of the present study constitute an advance in the available diagnostic methods for bacterial pathogens in fish farms.

关键词： Direct Colony PCR 16s rrna sequencing Bacterial Fish Pathogens

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Enterococcus faecalis provides protection during scavenging in carrion crow (Corvus corone)

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Zoological Research 2024年第3期45卷 451-463页

作者： Bin Hu Jia-Min Wang Qing-Xun Zhang Jing Xu Ya-Nan Xing Bo Wang shu-Yi Han Hong-Xuan He CAs Key Laboratory of Animal Ecology and Conservation Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China College of Life sciences University of Chinese Academy of SciencesBeijing 100049China Beijing Milu Ecological Research Center Beijing 102600China Beijing Capital International Airport Co. Ltd.Beijing 101300China

The gut microbiota significantly influences host physiology and provides essential ecosystem *** diet can affect the composition of the gut microbiota,the gut microbiota can also help the host adapt to specific dietary *** carrion crow(Corvus corone),an urban facultative scavenger bird,hosts an abundance of pathogens due to its scavenging *** this,carrion crows infrequently exhibit illness,a phenomenon related to their unique physiological *** present,however,the role of the gut microbiota remains incompletely *** this study,we performed a comparative analysis using 16s rrna amplicon sequencing technology to assess colonic content in carrion crows and 16 other bird species with different diets in Beijing,*** findings revealed that the dominant gut microbiota in carrion crows was primarily composed of Proteobacteria(75.51%)and Firmicutes(22.37%).significant differences were observed in the relative abundance of Enterococcus faecalis among groups,highlighting its potential as a biomarker of facultative scavenging behavior in carrion ***,*** isolated from carrion crows was transplanted into model mice to explore the protective effects of this bacterial community against salmonella enterica *** showed that *** down-regulated the expression of pro-inflammatory cytokines tumor necrosis factor alpha(TNF-α),interferon gamma(IFN-γ),and interleukin 6(IL-6),prevented *** colonization,and regulated the composition of gut microbiota in mice,thereby modulating the host’s immune regulatory ***,*** exerts immunoregulatory and anti-pathogenic functions in carrion crows engaged in scavenging behavior,offering a representative case of how the gut microbiota contributes to the protection of hosts with specialized diets.

关键词： Carrion crow Facultative scavenger Gut microbiota Enterococcus faecalis 16s rrna sequencing

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Bacterial community network complexity and role of stochasticity decrease during primary succession

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soil Ecology Letters 2024年第3期6卷 45-59页

作者： Yucheng He Binu M.Tripathi Jie Fang Zihao Liu Yaping Guo Yue Xue Jonathan M.Adams school of Geography and Ocean science Nanjing UniversityNanjing 210023China Korea Polar Research Institute Incheon 21990Republic of Korea

In microbial ecology,there is limited understanding of the mechanisms governing patterns in community structure across space and ***,we studied the changes of bacterial co-occurrence network structure over four primary successional soils after glacier retreat,including a sand dune system and three glacier foreland series,varying in timescale from centuries to *** found that in all series,network structure was most complex in the earliest stages of succession,and became simpler over *** and abundance of keystone species and network stability also declined over *** appears that with less productive,nutrient poor and physiologically extreme conditions of early succession,closer interactions among bacterial species are ecologically selected *** may take the form of consortia(with positive interactions)or stronger niche exclusion(with negative interactions).Additionally,we quantified the relative roles of different structuring processes on bacterial community using a bin-based null model analysis(iCAMP).With each successional series,community composition was initially governed by stochasticity,but as succession proceeded there was a progressive increase in deterministic selection over time,correlated with decreasing ***,our results show a consistency among the four series in long-term processes of community succession,with more integrated networks and greater stochasticity in early stages.

关键词： glacial retreat bacteria chronosequence co-occurrence network 16s rrna sequencing community assembly

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Intratumoural microorganism can affect the progression of hepatocellular carcinoma

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World Journal of Gastrointestinal Oncology 2024年第10期16卷 4232-4243页

作者： Bao-Qun Liu Yi Bai Da-Peng Chen Ya-Min Zhang Tian-Ze Wang Jing-Rui Chen Xiang-Yu Liu Bin Zheng Zi-Lin Cui First Central Clinical College Tianjin Medical UniversityTianjin 300070China Department of Hepatobiliary surgery Tianjin First Central HospitalSchool of MedicineNankai UniversityTianjin 300192China Tianjin First Central Hospital Clinic Institute School of MedicineNankai UniversityTianjin 300192China school of Medicine Tianjin UniversityTianjin 300072China

BACKGROUND several recent studies have confirmed that intratumoural microorganisms can affect the occurrence and development of hepatocellular carcinoma(HCC);however,their role in tumor progression remains ***,there is a need for further research on the role of intratumoural microorganisms in *** To investigate the changes in intratumoural microorganisms in HCC and the effect of Propionibacterium on HCC *** HCC and normal liver tissue specimens were subjected to fluorescence in situ hybridization(FIsH).After performing 16s rrna sequencing on HCC and peritumoral tissues to analyze the differences between the two *** was cocultured with HCC cells in *** in cell proliferation and migration capacity were *** expression of NF-κB pathway related proteins in tumor cells was *** orthotopic liver implantation model and the subcutaneous xenograft model were *** tissues and subcutaneous tumors were collected 2 weeks *** FIsH demonstrated the presence of microorganisms in HCC and normal liver tissues.16s rrna sequencing revealed an abundance of Lysobacter,Lachnospiraceae,Pseudomonas,and Lactobacillus in HCC *** distribution and abundance of Propionibacterium showed differences between HCC and peritumoral tissues(Pstudies demonstrated that Propionibacterium and its metabolite propionic acid(PA)inhibited the proliferation and migration of HCC cells(Pssion of the proteins in NF-κB signaling pathway also decreased in HCC cells(PsION Microorganisms in HCC and normal liver tissues displayed significant *** PA-producing bacterium Propionibacterium in HCC exerts an effect on the NF-κB pathway,thereby affecting the biological behavior of HCC.

关键词： Hepatocellular carcinoma Intratumoural microbiome 16s rrna sequencing Propionibacterium

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Bacterial communities associated with natural and commercially grown rooibos (Aspalathus linearis)

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Pedosphere 2020年第6期30卷 778-790页

作者： Casparus J.BRINK Anneke POsTMA Etienne sLABBERT Ferdinand POsTMA A.Muthama MUAsYA Karin JACOBs Department of Microbiology University of StellenboschPrivate Bag X1Stellenbosch 7600South Africa Central Analytical Facility University of StellenboschPrivate Bag X1Stellenbosch 7602South Africa Department of Biological sciences University of Cape TownPrivate Bag X3Rondebosch 7701South Africa

Aspalathus linearis is a commercially important plant species endemic to the Cape Floristic Region of south Africa and is used to produce a herbal tea known as rooibos *** interactions between *** and soil bacteria play an important role in the survival of Aspalathus plants in the highly nutrient-poor,acidic fynbos *** aim of this study was to characterize and compare rhizosphere and bulk soil bacterial communities associated with natural and commercially grown ***,as well as the effect of seasonal changes on these *** communities were characterized using high throughput amplicon sequencing,and their correlations with soil chemical properties were *** N-fixing bacterial community was characterized using terminal restriction fragment length polymorphism and real time quantitative polymerase chain ***,Proteobacteria,and Acidobacteria were the most dominant bacterial phyla detected in this *** similar bacterial communities were associated with natural and commercially grown *** differences in the bacterial community were observed between rhizosphere and bulk soils collected in the dry season,while no significant differences were detected in the wet *** study provides insights into bacterial community structure and potential factors shaping bacterial community structure with commercially important ***.

关键词： bulk soil fynbos N-fixing bacterial community operational taxonomic unit rhizosphere soil 16s rrna sequencing

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The Relationship Between the Gut Microbiome and Neurodegen-erative Diseases

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Neuroscience Bulletin 2021年第10期37卷 1510-1522页

作者： Xueling Zhu Bo Li Pengcheng Lou Tingting Dai Yang Chen Aoxiang Zhuge Yin Yuan Lanjuan Li state Key Laboratory for Diagnosis and Treatment of Infectious Diseases National Clinical Research Center for Infectious DiseasesCollaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesThe First Affiliated HospitalZhejiang University School of MedicineHangzhou 310003China Research Units of Infectious Disease and Microecology Chinese Academy of Medical SciencesBeijing 100730China The First Affiliated Hospital Zhejiang University School of MedicineHangzhou 310003China

Many recent studies have shown that the gut microbiome plays important roles in human physiology and ***,microbiome-based therapies have been used to improve health status and treat *** addition,aging and neurodegenerative diseases,including Alzheimer’s disease and Parkinson’s disease,have become topics of intense interest in biomedical *** researchers have explored the links between these topics to study the potential pathogenic or therapeutic effects of intestinal microbiota in *** the exact relationship between neurodegenerative diseases and gut microbiota remains *** technology advances,new techniques for studying the microbiome will be developed and refined,and the relationship between diseases and gut microbiota will be *** article summarizes the known interactions between the gut microbiome and neurodegenerative diseases,highlighting assay techniques for the gut microbiome,and we also discuss the potential therapeutic role of microbiome-based therapies in diseases.

关键词： Gut microbiome Neurodegenerative diseases Aging 16s rrna sequencing Multi-omics Microbiome-based therapies

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Assessing the microbiota of recycled bedding sand on a Wisconsin dairy farm

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Journal of Animal science and Biotechnology 2022年第2期13卷 601-612页

作者： Hannah E.Pilch Andrew J.steinberger Donald C.sockett Nicole Aulik Garret suen Charles J.Czuprynski Department of Pathobiological sciences School of Veterinary MedicineUniversity of Wisconsin-MadisonMadison 53706USA Department of Bacteriology University of Wisconsin-MadisonMadison 53706USA Microbiology Doctoral Training Program University of Wisconsin-MadisonMadison 53706USA Wisconsin Veterinary Diagnostic Laboratory School of Veterinary MedicineUniversity of Wisconsin-MadisonMadison 53706USA

Background:sand is often considered the preferred bedding material for dairy cows as it is thought to have lower bacterial counts than organic bedding materials and cows bedded on sand experience fewer cases of lameness and *** can also be efficiently recycled and reused,making it ***,some studies have suggested that the residual organic material present in recycled sand can serve as a reservoir for commensal and pathogenic bacteria,although no studies have yet characterized the total bacterial community *** we sought to characterize the bacterial community composition of a Wisconsin dairy farm bedding sand recycling system and its dynamics across several stages of the recycling process during both summer and winter using 16s rrna gene amplicon ***:Bacterial community compositions of the sand recycling system differed by both seasons and *** samples had higher richness and distinct community compositions,relative to winter *** both summer and winter samples,the diversity of recycled sand decreased with time drying in the recycling ***,summer sand 14 d post-recycling was enriched in operational taxonomic units(OTUs)belonging to the genera Acinetobacter and Pseudomonas,relative to freshly washed sand and sand from cow *** contrast,no OTUs were found to be enriched in winter *** sand recycling system contained an overall core microbiota of 141 OTUs representing 68.45%±10.33%sD of the total bacterial relative abundance at each sampled *** 4 most abundant genera in this core microbiota included Acinetobacter,Psychrobacter,Corynebacterium,and *** was present in greater abundance in summer samples,whereas Psychrobacter and Corynebacterium had higher relative abundances in winter *** had consistent relative abundances across both ***:These findings highlight the potential of recycled bedding sand as a bacterial reservo

关键词： Bovine Dairy farm Microbiota Recycled bedding sand 16s rrna sequencing

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Drought stress and plant ecotype drive microbiome recruitment in switchgrass rhizosheath

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Journal of Integrative Plant Biology 2021年第10期63卷 1753-1774页

作者： Tie-Yuan Liu Nenghui Ye Xinyu Wang Debatosh Das Yuxiang Tan Xiangkai You Mingxiu Long Tianming Hu Lei Dai Jianhua Zhang Mo-Xian Chen College of Grassland Agriculture Northwest A&F UniversityYangling 712100China Co-Innovation Center for sustainable Forestry in southern China College of Biology and the EnvironmentNanjing Forestry UniversityNanjing 210037China CAs Key Laboratory of Quantitative Engineering Biology Shenzhen Institute of Synthetic BiologyShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China southern Regional Collaborative Innovation Center for Grain and Oil Crops in China College of AgricultureHunan Agricultural UniversityChangsha 410128China state Key Laboratory of Agrobiotechnology The Chinese University of Hong KongShatinHong Kong 999077China Department of Biology Hong Kong Baptist UniversityKowloonHong Kong 999077China

The rhizosheath,a layer of soil grains that adheres firmly to roots,is beneficial for plant growth and adaptation to drought *** is a perennial C4 grass which can form contact rhizosheath under drought *** this study,we characterized the microbiomes of four different rhizocompartments of two switchgrass ecotypes(Alamo and Kanlow)grown under drought or well-watered conditions via 16s ribosomal RNA amplicon *** four rhizocompartments,the bulk soil,rhizosheath soil,rhizoplane,and root endosphere,harbored both distinct and overlapping microbial *** root compartments(rhizoplane and root endosphere)displayed low-complexity communities dominated by Proteobacteria and *** to bulk soil,Cyanobacteria and Bacteroidetes were selectively enriched,while Proteobacteria and Firmicutes were selectively depleted,in rhizosheath *** from Proteobacteria or Firmicutes were specifically selected in Alamo or Kanlow rhizosheath *** drought stress,Citrobacter and Acinetobacter were further enriched in rhizosheath soil,suggesting that rhizosheath microbiome assembly is driven by drought ***,the ecotype-specific recruitment of rhizosheath microbiome reveals their differences in drought stress ***,these results shed light on rhizosheath microbiome recruitment in switchgrass and lay the foundation for the improvement of drought tolerance in switchgrass by regulating the rhizosheath microbiome.

关键词： 16s rrna sequencing rhizosphere rhizosheath formation switchgrass(Panicum virgatum L.) water deficiency

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salmonella Typhimurium infection disrupts but continuous feeding of Bacillus based probiotic restores gut microbiota in infected hens

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Journal of Animal science and Biotechnology 2020年第3期11卷 789-804页

作者： samiullah Khan Kapil K.Chousalkar school of Animal and Veterinary sciences The University of AdelaideRoseworthySouth Australia 5371Australia

Background:The gut microbiota plays an important role in the colonisation resistance and invasion of *** Typhimurium has the potential to establish a niche by displacing the microbiota in the chicken gut causing continuous faecal shedding that can result in contaminated eggs or egg *** the current study,we investigated the dynamics of gut microbiota in laying chickens during salmonella Typhimurium *** optimisation of the use of an infeed probiotic supplement for restoration of gut microbial balance and reduction of salmonella Typhimurium load was also ***:salmonella infection caused dysbiosis by decreasing(FDRsuch as Blautia,Enorma,Faecalibacterium,shuttleworthia,sellimonas,Intestinimonas and subdoligranulum and increasing the abundance of genera such as Butyricicoccus,Erysipelatoclostridium,Oscillibacter and *** higher salmonella Typhimurium load resulted in lower(Psuch as Lactobacillus,Alistipes,Bifidobacterium,Butyricimonas,Faecalibacterium and Romboutsia suggesting salmonella driven gut microbiota *** salmonella load led to increased abundance of genera such as Caproiciproducens,Acetanaerobacterium,Akkermansia,Erysipelatoclostridium,Eisenbergiella,Escherichiashigella and Flavonifractor suggesting a positive interaction of these genera with salmonella in the displaced gut *** supplementation improved the gut microbiota by balancing the abundance of most of the genera displaced by the salmonella challenge with clearer effects observed with continuous supplementation of the *** levels of acetate and butyrate in the faeces were not affected(P>0.05)by salmonella challenge and the butyrate level was increased by the continuous feeding of the *** supplementation in salmonella challenged chickens resulted in higher level of *** probiotic supplementation decreased(P<0

关键词： 16s rrna sequencing Chicken gut microbiota Gut metabolites salmonella Typhimurium strategic feeding of probiotic

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