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Performance comparison of different microbial DNA extraction methods on bird feces

Avian Research 2021年第2期12卷 247-254页

作者： Xian Hou Shengkai Pan Zhenzhen Lin Jiliang Xu Xiangjiang Zhan School of Ecology and Nature Conservation Beijing Forestry UniversityBeijing 100083China Key Lab of Animal Ecology and Conservation Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Cardiff University-Institute of Zoology Joint Laboratory for Biocomplex-ity Research Chinese Academy of SciencesBeijing 100101China Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sci-encesKunming 650223China

Background:As an important player during food digestion,gut microbiota has attracted much attention in diet adaptation studies in *** extracted from feces has been widely used as a proxy for gut *** several methods have been developed for microbial DNA extraction,their performances in the bird feces have not been systematacially evaluated ***:In this study,we applied three DNA extraction methods(Qiagen,MoBio and Bead)to extract DNA from feces of three avian dietary guilds(granivore,omnivore and carnivore),sequenced V4 region of 16S rRNA gene for each extract and evaluated the performances of DNA yield,DNA integrity,microbial composition,cell lysis capacity and alpha diversity for the three methods on each dietary ***:Bead method was the best on the performance of both DNA yield and DNA integrity regardless of dietary *** granivore,microbial relative abundance at both species and phylum levels,alpha diversity and cell lysis capacity were comparable among all *** omnivore,Qiagen had the best performance on alpha diversity,fol-lowed by Bead and *** were small variations on microbial relative abundance at both species and phylum levels among different extraction *** exhibited the best performance on cell lysis *** carnivore,considerable variations were found on microbial relative abundance at both species and phylum *** had the best performance on alpha diversity,followed by MoBio and *** had the highest cell lysis ***:DNA yield and integrity have no obvious impact on microbial composition,alpha diversity or cell lysis *** microbiota results(e.g.,microbial composition,cell lysis capacity,alpha diversity)obtained from differ-ent methods are comparable in granivorous avian species but not in omnivorous or carnivorous *** method could be used in granivore microbiota *** omnivores and carnivores,we recommend Qiagen method when the

关键词： 16S rRNA Alpha diversity Avian Dietary guild feces DNA extraction method Microbial relative abundance

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Effects of feces on Spatial Distribution Patterns of Grazed Grassland Communities

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Agricultural Sciences in China 2010年第1期9卷 121-129页

作者： Tamanna Islam Eiki Fukuda Masae Shiyomi Molla Rahman Shaibur Shigenao Kawai Mikinori Tsuiki The United Graduate School of Agricultural Sciences Iwate UniversityMorioka 020-8550Japan National Agricultural Research Center for Tohoku Region Morioka 020-0198Japan Faculty of Science Ibaraki UniversityMito 310-8512Japan Department of Environmental Science and Health Management Jessore Science and Technology UniversityJessore 7400Bangladesh

Animals excrete feces during grazing. The uneven distribution of feces causes a spatial heterogeneity in grassland communities. In this study, we attempted to clarify the effects of feces on spatial distribution patterns of plant species. A field study was conducted on four grasslands each grazed by a single cow. These four grasslands were defined as Poa pratensis （Kentucky bluegrass） dominated grassland without feces （PoF-）, Poa pratensis dominated grassland with feces （PoF＋）, Zoysia japonica Steud. （Japanese lawngrass） dominated grassland without feces （ZyF-）, and Zoysia japonica Steud. dominated grassland with feces （ZyF＋）. A 50 m line that transects 100 equally spaced quadrats （L-quadrats） was drawn on each of the four grasslands. Each quadrat was 0.50 m × 0.50 m in size and consisted of four equal-area cells of 0.25 m ×0.25 m （S-quadrats）. The occurrences of all plant species were recorded in each S-quadrat. The binomial distribution （BD） and beta-binomial distribution （BBD） were used to represent the variation in spatial patterns. The BBD provided a significant description of the frequency distribution of plants per quadrat. A power law was used to calculate the spatial heterogeneity of each species together with the community heterogeneity. The results revealed that the plants on each of the four grasslands were aggregatively distributed. The ZyF＋ exhibited greater spatial heterogeneity than the ZyF-due to the uneven deposition of feces by cows grazing on the grasslands. Additionally we also found that the feces had effect on the heterogeneity inZyF＋ and did not have effect in PoF＋.

关键词： beta-binomial distribution power law feces grazing grassland spatial distribution

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Difference and clinical value of metabolites in plasma and feces of patients with alcohol-related liver cirrhosis

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World Journal of Gastroenterology 2023年第22期29卷 3534-3547页

作者： Yi-Fan Xu Yan-Xu Hao Lei Ma Meng-Han Zhang Xuan-Xuan Niu Yan Li Yuan-Yuan Zhang Ting-Ting Liu Ming Han Xiao-Xue Yuan Gang Wan Hui-Chun Xing Center of Liver Diseases Division 3 Beijing Ditan HospitalCapital Medical UniversityBeijing 100015China Beijing Key Laboratory of Emerging Infectious Diseases Institute of Infectious DiseasesBeijing Ditan HospitalCapital Medical UniversityBeijing 100015China Beijing Institute of Infectious Diseases Beijing Institute of Infectious DiseasesBeijing 100015China National Center for Infectious Diseases Beijing Ditan HospitalCapital Medical UniversityBeijing 100015China Department of Statistic Beijing Ditan HospitalCapital Medical UniversityBeijing 100015China Center of Liver Diseases Division 3 Beijing Ditan HospitalPeking University Ditan Teaching HospitalBeijing 100015China

BACKGROUND Alterations in plasma and intestinal metabolites contribute to the pathogenesis and progression of alcohol-related liver cirrhosis(ALC).AIM To explore the common and different metabolites in the plasma and feces of patients with ALC and evaluate their clinical *** According to the inclusion and exclusion criteria,27 patients with ALC and 24 healthy controls(HCs)were selected,and plasma and feces samples were *** function,blood routine,and other indicators were detected with automatic biochemical and blood routine *** chromatography-mass spectrometry was used to detect the plasma and feces metabolites of the two groups and the metabolomics of plasma and ***,the correlation between metabolites and clinical features was *** More than 300 common metabolites were identified in the plasma and feces of patients with *** analysis showed that these metabolites are enriched in bile acid and amino acid metabolic *** to HCs,patients with ALC had a higher level of glycocholic acid(GCA)and taurocholic acid(TCA)in plasma and a lower level of deoxycholic acid(DCA)in the feces,while L-threonine,L-phenylalanine,and L-tyrosine increased simultaneously in plasma and ***,TCA,L-methionine,L-phenylalanine,and L-tyrosine in plasma were positively correlated with total bilirubin(TBil),prothrombin time(PT),and maddrey discriminant function score(MDF)and negatively correlated with cholinesterase(CHE)and albumin(ALB).The DCA in feces was negatively correlated with TBil,MDF,and PT and positively correlated with CHE and ***,we established a P/S BA ratio of plasma primary bile acid(GCA and TCA)to fecal secondary bile acid(DCA),which was relevant to TBil,PT,and MDF *** The enrichment of GCA,TCA,L-phenylalanine,L-tyrosine,and L-methionine in the plasma of patients with ALC and the reduction of DCA in feces were related to the severity of *** metabolites may be used as ind

关键词： Alcohol-related liver cirrhosis Plasma feces Metabolites Deoxycholic acid Amino acids

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Biomarkers for hepatocellular carcinoma based on body fluids and feces

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World Journal of Gastrointestinal Oncology 2021年第5期13卷 351-365页

作者： Ming-Cheng Guan Wei Ouyang Ming-Da Wang Lei Liang Na Li Ting-Ting Fu Feng Shen Wan-Yee Lau Qiu-Ran Xu Dong-Sheng Huang Hong Zhu Tian Yang Department of Medical Oncology The First Affiliated Hospital of Soochow UniversitySuzhou 215006Jiangsu ProvinceChina Department of Hepatobiliary Surgery Eastern Hepatobiliary Surgery Hospital(Navy Medical University)Second Military Medical UniversityShanghai 200438China

Novel non-/minimally-invasive and effective approaches are urgently needed to supplement and improve current strategies for diagnosis and management of hepatocellular carcinoma(HCC).Overwhelming evidence from published studies on HCC has documented that multiple molecular biomarkers detected in body fluids and feces can be utilized in early-diagnosis,predicting responses to specific therapies,evaluating prognosis before or after therapy,as well as serving as novel therapeutic *** and analysis of proteins,metabolites,circulating nucleic acids,circulating tumor cells,and extracellular vesicles in body fluids(e.g.,blood and urine)and gut microbiota(e.g.,in feces)have excellent capabilities to improve different aspects of management of *** studies have been devoted in identifying more promising candidate biomarkers and therapeutic targets for diagnosis,treatment,and monitoring responses of HCC to conventional therapies,most of which may improve diagnosis and management of HCC in the *** review aimed to summarize recent advances in utilizing these biomarkers in HCC and discuss their clinical significance.

关键词： Hepatocellular carcinoma Biomarker Blood Urine feces Gut microbiota

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CTX-M producing Escherichia coli isolated from cattle feces in Bogor slaughterhouse,Indonesia

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Asian Pacific Journal of Tropical Biomedicine 2016年第7期6卷 605-608页

作者： Mirnawati Bachrum Sudarwanto Denny Widaya Lukman Hadri Latif Herwin Pisestyani Eddy Sukmawinata mer Akineden Ewald Usleber Laboratory of Veterinary Public Health Faculty of Veterinary MedicineBogor Agricultural University Veterinary Public Health Programme Veterinary Public HealthGraduate SchoolBogor Agricultural University Dairy Sciences Institute of Veterinary Food ScienceJustus-Liebig University Giessen

Objective: To determine the occurrence of CTX-M producing Escherichia coli(E. coli)from cattle feces in Bogor slaughterhouse, ***: A total of 220 cattle feces samples were collected from Bogor slaughterhouse from March to April 2015. Presence of extended-spectrum beta-lactamase(ESBL) producing E. coli was detected by disc diffusion test based on the recommendation from Clinical and Laboratory Standards Institute(2014). Bacterial strains which were confirmed as producing ESBLs were further analyzed for the presence of bla genes of the ESBL by ***: The results showed that CTX-M producing E. coli isolates were detected in 19 samples from 220 samples(8.6%). The b-lactamase genes detected were CTX-M-1(n = 10) and CTX-M-9(n = 9). All of the CTX-M producing E. coli isolates showed multidrug resistance phenotypes to at least four antibiotics. The highest incidence of antibiotics resistance was showed to ampicillin(100.0%), cefotaxime(100.0%), and cefpodoxime(100.0%), followed by streptomycin(84.3%), trimethoprim-sulfamethoxazole(73.7%), erythromycin(52.6%), kanamycin(26.3%), doxycycline(10.5%), and ceftazidime(0.0%).Conclusions: Detection of CTX-M-producing E. coli in cattle feces raises important questions as they can represent a potential risk factor to public health.

关键词： Cattle feces CTX-M Escherichia coli Slaughterhouse

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PHYTOPLANKTON,ESPECIALLY DIATOMS,IN THE GUT CONTENTS AND feces OF TWO PLANTIVOROUS CYPRINIDS-SILVER CARP AND BIGHEAD CARP

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Chinese Journal of Oceanology and Limnology 1994年第4期12卷 308-315页

作者：谢平刘建康 Donghu Experimental Station of Lake Ecosystems Institute of Hydrobiology Chinese Academy of Sciences Wuhan

In order to clarify whether the planktivorous silver carp and bighead carp can collect phytoplanktonas small as Cyclotella(<20μm)in Donghu Lake,studies on phytoplankton in their gut contents and feceswere made in ***... 详细信息

In order to clarify whether the planktivorous silver carp and bighead carp can collect phytoplanktonas small as Cyclotella(feceswere made in *** fish were cultured in both net cage in Donghu Lake and aquaria with the *** the intestine,the average valve diameter of Cyclotella changed *** average ratio of emptyfrustule of Cyclotella to total Cyclotella in the foregut contents of the fishes were 1.8—1.9 times higherthan that in the lake water,but changed little from foregut to *** aquarium experiment showedthat both carps could collect particles as small as 8-10μm, which was obviously narrower than the dis-tance between their gill ***,secretion of mucus plays an important role in collecting suchsmall

关键词： planktivorous fishes gut contents and feces diatoms valve diameter empty frustule

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A COVID-19 Patient Discharged According to Strict Discharge Standards:Viral Negativity in Both Nasopharynx and feces

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Infectious Diseases & Immunity 2022年第3期2卷 210-212页

作者： Enqiang Chen Lichun Wang Guangming Tang Menglan Wang Yachao Tao Ping Feng Hong Tang Center of Infectious Diseases West China Hospital of Sichuan UniversityChengdu 610041China

Severe acute respiratory syndrome Coronavirus 2(SARS-CoV-2)currently has spread all over the ***,the dynamic characteristics of SARS-CoV-2 infections have not previously been described in ***,we report a cured patient in West China Hospital,and describe the dynamic detection of SARS-CoV-2-RNA in different specimens and viral specific IgM and IgG antibodies in *** findings suggest that the fecal SARS-CoV-2-RNA negativity may be considered as a new standard for de *** IgM and IgG antibodies detection were helpful for early diagnosis of SARS-CoV-2 infection and judgment of patients in recovery stage,respectively.

关键词： feces IgG antibody IgM antibody SARS-CoV-2 Viral RNA

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A multi-criteria decision-making approach for comparing sample preservation and DNA extraction methods from swine feces

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American Journal of Molecular Biology 2012年第2期2卷 159-169页

作者： Sepideh Pakpour Abbas S. Milani Martin R. Chénier Department of Animal Science McGill University Montreal Canada Department of Food Science and Agricultural Chemistry McGill University Montreal Canada School of Engineering University of British Columbia-Okanagan Kelowna Canada

Molecular microbiological methods, such as competetive PCR, real-time PCR, denaturing gradient gel electrophoresis (DGGE) and large-scale parallel-pyrosequencing, require the extraction of sufficient quantity of high quality DNA from microbiologically and chemically complex matrices. Due to difficulties in the field to standardize/select the optimum DNA preservation-extraction methods in view of laboratories differences, this article attempts to present a straight-forward mathematical framework for comparing some of the most commonly used methods. To this end, as a case study, the problem of selecting an optimum sample preservation-DNA extraction strategy for obtaining total bacterial DNA from swine feces was considered. Two sample preservation methods (liquid nitrogen and RNAlater?) and seven extraction techniques were paired and compared under six quantitative DNA analysis criteria: yield of extraction, purity of extracted DNA (A260/280 and A 260/230 ratios), duration of extraction, degradation degree of DNA, and cost. From a practical point of view, it is unlikely that a single sample preservation-DNA extraction strategy can be optimum for all selected criteria. Hence, a systematic multi-criteria decision-making (MCDM) approach was used to compare the methods. As a result, the ZR Fecal DNA MiniPrepTM DNA extraction kit for samples preserved either with liquid nitrogen or RNAlater? were identified as potential optimum solutions for obtaining total bacterial DNA from swine feces. Considering the need for practicality for in situ applications, we would recommend liquid nitrogen as sample preservation method, along with the ZR Fecal DNA MiniPrepTM kit. Total bacterial DNA obtained by this strategy can be suitable for downstream PCR-based DNA analyses of swine feces.

关键词： Sample Preservation DNA Extraction Swine feces Multi-Criteria Decision-Making Weighed Sum Method

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Screening and analysis of metabolic components in rat urine and feces after oral administration of total glycosides of Jinkuishenqi pills by HPLC-ESI/MSn

Screening and analysis of metabolic components in rat urine ...

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第十四届全国中药和天然药物学术研讨会

作者： LI Wen-Lan BAI Jing HU Yang Jl Yu-Bin DU Juan SUN Zhi Research Center on Life Sciences and Environmental Sciences Harbin University of Commerce Engineering Research Center of Natural Anticancer Drugs Ministry of Education

AIM:To identify the chemical components of the total glycosides(TG) of Jinkuishenqi pills and their metabolites ***:An HPLC-ESI-MS method was developed for analysis of the metabolites of TG in rat plasma,after the rat was administered with the ***:A total of 18 compounds were detected in urine after oral administration of TG,nine of which are metabolites and the others are the original form of the compounds contained in Jinkuishenqi *** them,the metabolites are gallic acid,dehydromorroniaglycone,2-hydroxyacetophenone-4-0-glucuronic acid esters,paeonimetabolin I,Mlog-2,Mlog-1,2-hydroxy-4-methoxy acetophenone-5-O-sulfate,2,4-dihydroxyacetophenone and one unknown compound,respectively.A total of 20 compounds were detected in the feces after oral administration of TG,eight of which are metabolites and the others are the original form of the compounds contained in Jinkuishenqi *** them,the metabolites are gallic acid,swerosimetabolin A,paeonimetabolin I,Mlog-2,Mmor-2,Mlog-1 and two unknown ***:Using HPLC-ESI-MS,it was possible to screen and analyze the multiple compounds and metabolites of TG in vivo of *** identification and structure elucidation of these metabolites provided essential data for further pharmacological and mechanism of effectiveness of TG.

关键词： Jinkuishenqi pills Total glycosides In vivo metabolites urine feces HPLC-ESI/MS

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Nitrogen and fiber concentration in rumen contents and fecescontents of Mongolian gazelles

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Journal of Forestry Research 1999年第2期10卷 103-106页

作者：马建章李俊生姜兆文顾明波

Fecal indicators of nutritional status of wild ungulates were less constrained than that of blood, rumen contents, or urine analyses. Thus, we compared the nitrogen and fiber concentrations of feces with those of the rumen contents of Mongolian gazelles (Procapra guttrurosa) in Hulunbeier Grassland. Rumen contents and fecal nutritional concentrations varied in different seasons. Dietary nitrogen concentrations only increased linearly with increase nitrogen concentration in fecal in winter. There was a positive correlation between rumen NDF (neutral detergent fiber) and fecal NDF concentrations. But the regression coefficient was small (r=0.3917). There was a significant regression equation between rumen contents ADF (acid detergent fiber) and fecal ADF concentrations,as well as ADL (acid detergent lignin) concentrations. Nitrogen concentration was found to be negatively correlated with NDF ADF and ADL concentrations both in rumen and in fecal compositions. Our data suggest that fecal nitrogen, ADF ADL concentrations may assess winter dietary qualities that are in protein, crude fiber and lignin concentrations for Mongolian gazelles.

关键词： Procapra guttrurosa Rumen content feces Nitrogen concentration Fiber concentration

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