The authors would like to acknowledge Latoya Wiggins and Katelyn Griffin for their assistance in sample acquisition, as well as Laura Lee Rutherford for their assistance in sampling and molecular analyses. We would also like to thank Sarah Owens from Argonne National Lab for microbiomic sample preparation and sequencing. These investigations were supported equally by the Agricultural Research Service, USDA CRIS Projects &#8220;Pathogen Reduction and Processing Parameters in Poultry Processing Systems&#8221; #6612-41420-017-00 and &#8220;Molecular Approaches for the Characterization of Foodborne Pathogens in Poultry&#8221; #6612-32000-059-00.

환경 가금류 생산 샘플 1. 기계 균질화 <ol style="margin-left: 40px;"><li> 추출에 앞서, 95 ° C 수욕을 설정하고 수조 시간은 그 온도에 도달 할 수있다. </li><li> 2 ml의 용균 매트릭스 E 관에 흙이나 배설물의 0.33 g을 달다. <ol><li> 이 튜브의 용량을 초과 다음 해결책에 따라 발생할 수 있기 때문에, 튜브 샘플의 0.33 g을 초과하지 마십시오. </li><li> RT에 해동 냉동 샘플 무게 전에. </li><li> 토양 / 대변의 1g 총을 분석하기 위해, 아웃 셋 무게 개별 환경 시료 0.33 g 샘플을 복제. </li><li> 사전에 추출 원추형 매트릭스 관내 -20 ° C에서 샘플들을 저장이 필요할 경우. </li></ol></li><li> 825 μL 나트륨 인산염 버퍼 및 샘플 튜브에 PLS 솔루션의 275 μl를 추가합니다. ~ 15 초 동안 소용돌이를 사용하여 혼합 한 후 5 분 동안 14,000 XG에서 원심 분리. </li><li> superna을 가만히 따르다TANT은 버퍼 ASL 700 μl를 추가합니다. 5 초 동안 소용돌이를 사용하여 혼합한다. <ol><li> 헤드 스페이스는이 시점에서 원뿔 튜브에서 사용할 수있는 (~ 10 %의 총 부피)이 있는지 확인하십시오. 상층에 빈 공간이없는 경우, 튜브는 교차 오염 및 / 또는 샘플의 손실을 초래할 수있는 다음 균질화 단계 중에 누출되는 경향을 가질 것이다. </li></ol></li><li> FastPrep (24) 악기로 샘플을 놓고 40 초 동안 6.0 m / sec의 속도로 샘플을 균질화. </li><li> 5 분 동안 14,000 XG에서 균질화 된 샘플을 원심 분리기. 멸균이 ML의 microcentrifuge 관에 뜨는을 전송합니다. </li><li> 샘플에서 DNA 복구를 극대화하기 위해, 반복 같은 멸균, 2 ML의 microcentrifuge 관에 상층 액을 결합, 1.6 1.4 단계를 반복합니다. </li></ol> 샘플의 균질에서 억제 2. 효소 억제 참고 :이 프로토콜은 QIAamp DNA 의자 미니 키트를 사용합니다. <ol style="margin-left: 40px;"><li> 품어5 분 동안 95 ° C의 물욕 상등액 상등액 내의 나머지 세포로부터 DNA 복구를 최대화한다. <ol><li> 대부분 그람 음성 미생물을 함유하는 샘플을 70 ℃에서 배양한다. 그람 양성균이 (가금류 배설물 샘플의 경우입니다) 존재하는 경우, 95 ° C에서 배양한다. </li><li> 압력이 밀봉 된 마이크로 원심 튜브에 구축 할 수있는 튜브가 열려 &quot;팝업&quot;되지 않도록하고 잠재적으로 샘플 볼륨을 잃고 마이크로 원심 튜브에 플라스틱 잠금 클립을 사용합니다. </li></ol></li><li> 압력, 다시 캡 마이크로 원심 튜브를 해제하고 15 초 동안 소용돌이를 사용하여 혼합 각 microcentrifuge 관을 엽니 다. </li><li> 1 분 동안 14,000 XG에서 샘플을 원심 분리기 상층 액의 1.2 ml의를 제거하고 새 멸균 2 ml의 microcentrifuge 관에 배치합니다. </li><li> 각 샘플 1 InhibitEx 탭을 추가하고 샘플을 균일하게 흰색 / 오프 하얀 액체가 될 때까지 소용돌이를 사용하여 섞는다. <ol><li> t을 피샘플을 포함하는 microcentrifuge 관으로 배치하면서 InhibitEx 탭을 ouching. 이를 위해 오픈 microcentrifuge 관 바로 위에 탭을 포함하는 블리스 터 팩을 배치하고 부드럽게 블리스 터 팩에서 그리고 microcentrifuge 관에 탭을 누릅니다. </li></ol></li><li> 5 분 동안 14,000 XG에서 RT (~ 25 ° C에서)에서 1 분 샘플과 원심 분리기를 품어. </li><li> 5 분 동안 14,000 XG에서 멸균 1.5 ml의 microcentrifuge 관과 원심 분리기에 모든 액체를 전송합니다. <ol><li> 액체를 전송할 때 단계 2.5의 끝에 microcentrifuge 관 하단의 펠릿 수도있는 나머지 미립자를 피한다. </li></ol></li></ol> QIAcube 로봇 워크 스테이션을 사용하여 3. 자동화 된 DNA 정제 주 : 플라스틱 소모품의 개수, 원심 분리기 내에서 샘플 로터 어댑터의 배치, 및 완충제 / 용액의 필요한 볼륨 NUM에 의존실행 중입니다 샘플의 BER. <ol style="margin-left: 40px;"><li> 회 전자 어댑터 내에서 해당 슬롯에 용출 튜브 및 필터 튜브를 추가합니다. 각 샘플에 대해, 로터의 중간 어댑터 슬롯에 400 μL를 추가한다. 샘플 수에 따라 정제하지 올바른 배열로 워크 스테이션에서 원심 로터 어댑터를 놓는다. <ol><li> 실패가 정화 프로토콜의 원심 분리 단계 중 하나 동안 전단을 초래할 수 그렇게 때문에 microcentrifuge 관 뚜껑이 모두 제대로 로터 어댑터 내에 고정되어 있는지 확인합니다. </li></ol></li><li> 워크 스테이션에 1,000 μL, 200 μL 필터 - 팁 필요한 수를 추가하고 버퍼의 필요한 양을 가진 제공하는 버퍼의 병을 채 웁니다. 참고 :이 정화 프로토콜 (AL, AW1, AW2 및 AE)에 필요한 버퍼가 모든 QIAamp DNA 의자 미니 키트에 포함되어 있습니다. 사용자는 AW의 BU에 필요한 100 % 에탄올을 공급해야ffers 및 정제 공정에 사용되는 용액으로서. </li><li> 멸균 1.5 ml의 microcentrifuge 관에 공급 된 단백질 분해 효소 K 솔루션의 필요한 볼륨을 추가하고 워크 스테이션 슬롯에 배치합니다. 또한, 워크 스테이션의 통 부분을 2ml의 안전한 잠금 마이크로 원심 샘플 튜브의 RB (정제되는 샘플의 수와 같다) 필요한 번호를 추가한다. <ol><li> 샘플 튜브의 뚜껑이 제대로 시스템이 초기에 필요한 모든 플라스틱과 액체가 요청에 사용할 수 있는지 확인하기 위해 워크 스테이션을 검사 할 때 오류가 발생합니다 그렇게 실패 이후, 워크 스테이션의 해당 슬롯에 배치되어 있는지 확인합니다 실행합니다. </li></ol></li><li> 병원체 탐지 프로토콜 및 워크 스테이션이 제대로 장착되었는지 확인하기 위해 이후의 화면을 읽기 - 인간 의자를 - 워크 스테이션에 터치 스크린을 사용하여, DNA 의자를 선택합니다. 일단 모든 검사 화면이 프로토콜을 실행하려면 시작을 전달됩니다. <ol><li> 12 개 이상의 샘플에서 DNA를 추출하면 12 샘플의 실행이 워크 스테이션에 완료 ~ 72 분을 소요하기 때문에, 샘플의 다음 세트의 균질화 과정 (1 단계)을 시작합니다. </li></ol></li><li> 이후의 다운 스트림 분석에 필요한 때까지 -20 ° C에서, 회 전자 어댑터에서 샘플을 제거 그들을 모자, 장소. <ol><li> 이때, 원심 분리 / 증발 - 기반 시스템을 사용하여 개개의 샘플 (총 분석 량 = 1g) 미국 3 복제 정제를 결합. ETDA 트리스 완충액 100 ㎕의 최종 부피로 복제하고 용출액을 다시 결합한다. </li></ol></li></ol>

<ol>
	<li>Maukonen, J., Simoes, C., Saarela, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+currently+used+commercial+DNA-extraction+methods+give+different+results+of+clostridial+and+actinobacterial+populations+derived+from+human+fecal+samples.">The currently used commercial DNA-extraction methods give different results of clostridial and actinobacterial populations derived from human fecal samples.</a> FEMS microbiology ecology. 79, 697-708 (2012).</li><li>Tang, J. N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+effective+method+for+isolation+of+DNA+from+pig+faeces+and+comparison+of+five+different+methods.">An effective method for isolation of DNA from pig faeces and comparison of five different methods.</a> Journal of microbiological. 75, 432-436 (2008).</li><li>McOrist, A. L., Jackson, M., Bird, A. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+comparison+of+five+methods+for+extraction+of+bacterial+DNA+from+human+faecal+samples.">A comparison of five methods for extraction of bacterial DNA from human faecal samples.</a> Journal of microbiological. 50, 131-139 (2002).</li><li>Ariefdjohan, M. W., Savaiano, D. A., Nakatsu, C. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparison+of+DNA+extraction+kits+for+PCR-DGGE+analysis+of+human+intestinal+microbial+communities+from+fecal+specimens.">Comparison of DNA extraction kits for PCR-DGGE analysis of human intestinal microbial communities from fecal specimens.</a> Nutrition journal. 9, 23 (2010).</li><li>Carrigg, C., Rice, O., Kavanagh, S., Collins, G., O'Flaherty, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA+extraction+method+affects+microbial+community+profiles+from+soils+and+sediment.">DNA extraction method affects microbial community profiles from soils and sediment.</a> Applied microbiology and biotechnology. 77, 955-964 (2007).</li><li>Smith, B., Li, N., Andersen, A. S., Slotved, H. C., Krogfelt, K. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optimising+Bacterial+DNA+Extraction+from+Faecal+Samples:+Comparison+of+Three+Methods.">Optimising Bacterial DNA Extraction from Faecal Samples: Comparison of Three Methods.</a> The Open microbiology journal. 5, 14-17 (2011).</li><li>Claassen, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+comparison+of+the+efficiency+of+five+different+commercial+DNA+extraction+kits+for+extraction+of+DNA+from+faecal+samples.">A comparison of the efficiency of five different commercial DNA extraction kits for extraction of DNA from faecal samples.</a> Journal of microbiological. 94, 103-110 (2013).</li><li>Scupham, A. J., Jones, J. A., Wesley, I. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparison+of+DNA+extraction+methods+for+analysis+of+turkey+cecal+microbiota.">Comparison of DNA extraction methods for analysis of turkey cecal microbiota.</a> Journal of applied microbiology. 102, 401-409 (2007).</li><li>Salonen, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparative+analysis+of+fecal+DNA+extraction+methods+with+phylogenetic+microarray:+effective+recovery+of+bacterial+and+archaeal+DNA+using+mechanical+cell+lysis.">Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis.</a> Journal of microbiological methods. 81, 127-134 (2010).</li><li>Peng, X., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparison+of+direct+boiling+method+with+commercial+kits+for+extracting+fecal+microbiome+DNA+by+Illumina+sequencing+of+16S+rRNA+tags.">Comparison of direct boiling method with commercial kits for extracting fecal microbiome DNA by Illumina sequencing of 16S rRNA tags.</a> Journal of microbiological. 95, 455-462 (2013).</li><li>Yuan, S., Cohen, D. B., Ravel, J., Abdo, Z., Forney, L. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evaluation+of+methods+for+the+extraction+and+purification+of+DNA+from+the+human+microbiome.">Evaluation of methods for the extraction and purification of DNA from the human microbiome.</a> PloS one. 7, 33865 (2012).</li><li>Qu, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparative+Metagenomics+Reveals+Host+Specific+Metavirulomes+and+Horizontal+Gene+Transfer+Elements+in+the+Chicken+Cecum+Microbiome.">Comparative Metagenomics Reveals Host Specific Metavirulomes and Horizontal Gene Transfer Elements in the Chicken Cecum Microbiome.</a> PloS one. 3, 2945 (2008).</li><li>Sekelja, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Abrupt+temporal+fluctuations+in+the+chicken+fecal+microbiota+are+explained+by+its+gastrointestinal+origin.">Abrupt temporal fluctuations in the chicken fecal microbiota are explained by its gastrointestinal origin.</a> Applied and environmental microbiology. 78, 2941-2948 (2012).</li><li>Oakley, B. B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Poultry-Associated+Microbiome:+Network+Analysis+and+Farm-to-Fork+Characterizations.">The Poultry-Associated Microbiome: Network Analysis and Farm-to-Fork Characterizations.</a> PloS one. 8, 57190 (2013).</li><li>Cook, K. L., Rothrock, M. J., Eiteman, M. A., Lovanh, N., Sistani, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evaluation+of+nitrogen+retention+and+microbial+populations+in+poultry+litter+treated+with+chemical,+biological+or+adsorbent+amendments.">Evaluation of nitrogen retention and microbial populations in poultry litter treated with chemical, biological or adsorbent amendments.</a> Journal of environmental management. 92, 1760-1766 (2011).</li><li>Rothrock, M. J., Cook, K. L., Warren, J. G., Eiteman, M. A., Sistani, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microbial+mineralization+of+organic+nitrogen+forms+in+poultry+litters.">Microbial mineralization of organic nitrogen forms in poultry litters.</a> Journal of environmental quality. 39, 1848-1857 (2010).</li><li>Rothrock, M. J., Cook, K. L., Warren, J. G., Sistani, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+effect+of+alum+addition+on+microbial+communities+in+poultry+litter.">The effect of alum addition on microbial communities in poultry litter.</a> Poultry science. 87, 1493-1503 (2008).</li><li>Li, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evaluation+of+QIAamp+DNA+Stool+Mini+Kit+for+ecological+studies+of+gut+microbiota.">Evaluation of QIAamp DNA Stool Mini Kit for ecological studies of gut microbiota.</a> Journal of microbiological. 54, 13-20 (2003).</li><li>Dridi, B., Henry, M., El Khechine, A., Raoult, D., Drancourt, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High+precalence+of+Methanobrevibacter+smithii+and+Methanosphaera+stadtmanae+detected+in+the+human+gut+using+an+improved+DNA+detection+protocol.">High precalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol.</a> PloS one. 4, 7063 (2009).</li><li>Harms, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Real-time+PCR+quantification+of+nitrifying+bacteria+in+a+municipal+wastewater+treatment+plant.">Real-time PCR quantification of nitrifying bacteria in a municipal wastewater treatment plant.</a> Environmental science and technology. 37, 343-351 (2003).</li><li>Rothrock, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparison+of+microvolume+DNA+quantification+methods+for+use+with+volume-sensitive+environmental+DNA+extracts.">Comparison of microvolume DNA quantification methods for use with volume-sensitive environmental DNA extracts.</a> Journal of natural and environmental sciences. 2, 34-38 (2011).</li><li>Navas-Molina, J. A., DeLong Edward, F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Methods in Enzymology. 531, 371-444 (2013).</li><li>Caporaso, J. G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ultra-high-throughput+microbial+community+analysis+on+the+Illumina+HiSeq+and+MiSeq+platforms.">Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms.</a> The ISME journal. 6, 1621-1624 (2012).</li><li>Caporaso, J. G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Global+patterns+of+16S+rRNA+diversity+at+a+depth+of+millions+of+sequences+per+sample.">Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.</a> Proceedings of the National Academy of Sciences of the United States of America. 108 Suppl 1, 4516-4522 (2011).</li><li>Caporaso, J. G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=QIIME+allows+analysis+of+high-throughput+community+sequencing+data.">QIIME allows analysis of high-throughput community sequencing data.</a> Nature methods. 7, 335-336 (2010).</li><li>Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C., Knight, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=UCHIME+improves+sensitivity+and+speed+of+chimera+detection.">UCHIME improves sensitivity and speed of chimera detection.</a> Bioinformatics. 27, 2194-2200 (2011).</li><li>Edgar, R. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Search+and+clustering+orders+of+magnitude+faster+than+BLAST.">Search and clustering orders of magnitude faster than BLAST.</a> Bioinformatics. 26, 2460-2461 (2010).</li><li>DeSantis, T. Z., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Greengenes,+a+chimera-checked+16S+rRNA+gene+database+and+workbench+compatible+with+ARB.">Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.</a> Applied and environmental microbiology. 72, 5069-5072 (2006).</li><li>Caporaso, J. G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=PyNAST:+a+flexible+tool+for+aligning+sequences+to+a+template+alignment.">PyNAST: a flexible tool for aligning sequences to a template alignment.</a> Bioinformatics. 26, 266-267 (2010).</li><li>Price, M. N., Dehal, P. S., Arkin, A. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=FastTree+2&#8211;approximately+maximum-likelihood+trees+for+large+alignments.">FastTree 2&#8211;approximately maximum-likelihood trees for large alignments.</a> PloS one. 5, 9490 (2010).</li><li>Cook, K. L., Rothrock, M. J., Lovanh, N., Sorrell, J. K., Loughrin, J. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spatial+and+temporal+changes+in+the+microbial+community+in+an+anaerobic+swine+waste+treatment+lagoon.">Spatial and temporal changes in the microbial community in an anaerobic swine waste treatment lagoon.</a> Anaerobe. 16, 74-82 (2010).</li><li>Cook, K. L., Rothrock, M. J., Warren, J. G., Sistani, K. R., Moore, P. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effect+of+alum+treatment+on+the+concentration+of+total+and+ureolytic+microorganisms+in+poultry+litter.">Effect of alum treatment on the concentration of total and ureolytic microorganisms in poultry litter.</a> Journal of environmental quality. 37, 2360-2367 (2008).</li><li>Lovanh, N., Cook, K. L., Rothrock, M. J., Miles, D. M., Sistani, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spatial+shifts+in+microbial+population+structure+within+poultry+litter+associated+with+physicochemical+properties.">Spatial shifts in microbial population structure within poultry litter associated with physicochemical properties.</a> Poultry science. 86, 1840-1849 (2007).</li></ol>

The authors have nothing to disclose.

사용 된 DNA 추출법 샘플 이전 1,3,6- 본 DNA 추출법의 종속 특성을 분석지지 모두 분변 샘플 및 깔짚 정량적 총 세균 커뮤니티 추정치들을 달성. 배설물과 쓰레기 샘플 모두를 들어, DNA 추출 방법의 성능의 순서는 정량적 (기계&gt; 하이브리드&gt; 효소)과 정성 (효소&gt; 하이브리드&gt; 기계) 총 세균 지역 사회 추정치 달랐다. 하이브리드 방법은 높은 정량 또는 정성적인 추정치를 생성하지 않는...

When analyzing complex clinical or environmental samples (e.g., feces, soils), there are two main methodologies used for the extraction of DNA. The first is a mechanical disruption of the matrix using an intense bead-beating step, while the second is an enzymatic disruption of the matrix to chemically release bacterial cells and inhibit PCR inhibitors from the matrix simultaneously. Given the different means by which these two types of extraction methods work, it is not surprising that previous studies demonstrated that the appropriate DNA extraction method is both highly sample and analysis dependent. Comparative DNA extraction studies previously showed that some methods are more appropriate for improved DNA quality and quantity from environmental samples1-3, while others demonstrated improvements for community-level analyses such as denaturing gradient gel electrophoresis (DGGE)4-6, terminal restriction fragment length polymorphism (T-RFLP)7, automated ribosomal intergenic spacer analysis (ARISA)8, and phylogenetic microarrays9. Therefore, appropriate DNA extraction methods need to be used, or developed, according to the types of environmental samples and the types of analyses being performed on those samples, especially given the recent advancements in bacterial community analyses. 
Next generation sequencing, in conjunction with more quantitative community assessments (e.g., quantitative PCR (qPCR)), is becoming more prevalent in the environmental and clinical sciences, however, very little research has been performed to determine the effect of DNA extraction methods on these data sets. Most DNA extraction comparison studies dealt with microbiomic community estimates from human or human model samples10,11, not agricultural animal samples. The few poultry-focused next generation sequencing studies dealt with specific metagenomic12,13 or microbiomic14 questions; they did not discuss the effect of DNA extraction method on the resulting microbiomic analyses. Considering the complex nature of environmental samples related to poultry production (e.g., feces, litter/bedding, pasture soil), DNA extraction methods need to be carefully selected. Poultry-related environmental samples are known to contain large numbers of PCR inhibitors and up to 500-fold DNA extract dilutions have been required for PCR and subsequent downstream analysis15-17. Therefore it is essential that DNA extraction methods be optimized for these types of samples in order to not only physically disrupt the matrix, but also to be able to reduce/eliminate the large number of inhibitors that are present. 
The QIAamp DNA Stool Mini Kit, an enzymatic extraction method, has been considered the &#8220;gold standard&#8221; when extracting DNA from difficult gut/fecal samples1,18,19 and has been applied successfully to poultry environmental samples8,14. The enzymatic removal of PCR inhibitors through the use of a proprietary matrix is one of the greatest advantages of using this method for these types of environmental samples, as is the ability to significantly improve throughput (and reduce sample processing error) using automated workstations. One major disadvantage is the lack of a mechanical homogenization step to physically disassociate bacterial cells from the environmental matrix. When testing gut and fecal samples of non-poultry origin, the addition of a bead-beating or mechanical disruption step within a DNA extraction protocol significantly increased extraction efficiency9, DNA yield/quality1,4,5 and significantly improved downstream community analyses in terms of richness, diversity, and coverage5,6,11. These studies compared not only mechanical bead-beating methods to the &#8220;gold standard&#8221; enzymatic method, but some also added the mechanical bead-beating step to the enzymatic protocol to improve results6,9,11. 
According to the results from the above studies, bacterial community analyses (both qualitative and quantitative) could be improved from poultry-related environmental samples through the addition of a mechanical homogenization step to the enzymatic method. Therefore, the goal of this study was twofold: (1) to develop a novel DNA extraction technique that utilizes the most desirable aspects of both the mechanical (powerful homogenization step) and enzymatic (PCR inhibitor removal and automation) extraction methods and (2) compare the quantitative (via qPCR) and qualitative (via microbiomics) bacterial community assessments of this novel method to representative mechanical and enzymatic methods.

<table border="0" cellpadding="0" cellspacing="0" width="573">
	<tbody>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Name of Material/ Equipment</td>
			<td style="width:71px;">Company</td>
			<td style="width:119px;">Catalog Number</td>
			<td style="width:167px;">Comments/Description</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Lysing Matrix E tube</td>
			<td style="width:71px;">MPBio</td>
			<td style="width:119px;">6914-050</td>
			<td>Different sizes available and the last 3 numbers of the cat. No. indicate size (-050 = 50 tubes, -200 = 200 tubes, -1000 = 1000 tubes)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Sodium Phosphate Solution</td>
			<td style="width:71px;">MPBio</td>
			<td style="width:119px;">6570-205</td>
			<td>Can be purchased individually, or also contained within the FastDNA Spin Kit for Feces (Cat. No. 116570200)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">PLS Buffer</td>
			<td style="width:71px;">MPBio</td>
			<td style="width:119px;">6570-201</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Buffer ASL (560 ml)</td>
			<td style="width:71px;">Qiagen</td>
			<td align="right" style="width:119px;">19082</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">FastPrep 24 homogenizer</td>
			<td style="width:71px;">MPBio</td>
			<td align="right" style="width:119px;">116004500</td>
			<td>48 x 2 ml HiPrep adapter (Cat. No. 116002527) available to double throughput of mechanical homogenization step</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">QIAamp DNA Stool Mini Kit</td>
			<td style="width:71px;">Qiagen</td>
			<td align="right" style="width:119px;">51504</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">QIAcube24 (110V)</td>
			<td style="width:71px;">Qiagen</td>
			<td align="right" style="width:119px;">9001292</td>
			<td>Preliminary results show that QIAcube HT (Cat. No. 9001793) can be used to improve throughput, but different consumables are required of this machine and more comparative work needs to be done.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Filter-Tips, 1000 ml (1024)</td>
			<td style="width:71px;">Qiagen</td>
			<td align="right" style="width:119px;">990352</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Filter-Tips, 200 ml (1024)</td>
			<td style="width:71px;">Qiagen</td>
			<td align="right" style="width:119px;">990332</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">QIAcube Rotor Adapters (10 x 24)</td>
			<td style="width:71px;">Qiagen</td>
			<td align="right" style="width:119px;">990394</td>
			<td>For 1.5 ml microcentrifuge tubes included with in the rotor adapter kit there is an alternative.&#160; It is Sarstedt Micro tube 1.5 ml Safety Cap, Cat. No. 72.690</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Sample Tubes RB (2 ml)</td>
			<td style="width:71px;">Qiagen</td>
			<td align="right" style="width:119px;">990381</td>
			<td>Alternative: Eppendorf Safe-Lok micro test tube, Cat. No. 022363352</td>
		</tr>
	</tbody>
</table>

a hybrid dna extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples

DNA 추출 프로토콜의 효능을 조사되는 시료의 종류와 분석을 수행 하류의 두 종류에 따라 크게 좌우 될 수있다. 새로운 세균 지역 사회 분석 기술 (예를 들어, microbiomics, 메타 지노믹스)의 사용이 분야 내에서 농업과 환경 과학 및 많은 환경 시료에서 더욱 확산되고 있음을 감안하면 물리 화학적 및 미생물 (독특한에서 예를 들어, 배설물과 쓰레기 / 침구 샘플이 될 수 있습니다 가금류 생산 스펙트럼), 적절하고 효과적인 DNA 추출 방법이 신중하게 선택되어야한다. 따라서, 신규 한 반자동 하이브리드 DNA 추출법 환경 가금류 생산 샘플을 사용하기 위해 특별히 개발되었다. 기계적 및 효소 :이 방법은 DNA 추출의 두 가지 주요 유형의 조합이다. 두 단계의 격렬한 기계적 균질화 공정 (비드를 사용하여 고해 구체적 environmen 제형분변 샘플 시료 매트릭스로부터 박테리아를 제거하고 DNA를 향상과 그람 양성 세균 커뮤니티 회원 복구를 향상시키기 위해 탈 샘플)을 &quot;황금 표준&quot;효소 DNA 추출법의 시작 부분에 첨가 하였다. 하이브리드 방식의 효소 추출 부 개시하고 나면, 나머지 정제 공정은 시료 처리량을 증가시키고 시료 처리 오류를 감소시키는 로봇 자동화 된 워크 스테이션을 사용 하였다. 가금류의 배설물과 쓰레기 샘플을 처리 할 때 엄격한 기계 및 효소 DNA 추출 방법에 비해,이 소설 하이브리드 방법은 정량적 고려 전반적으로 최상의 성능을 결합 총 세균 지역 사회의 추정 (microbiomics 사용) (16S rRNA 유전자 qPCR에 사용)과 정성을 제공 .

이 연구를 위해 신선한 배설물 배설물과 쓰레기 샘플은 미국 남동부에있는 상업 육계 (~ 25,000 조류)에서 발견되었다. 육계 (루스 루스) 콥-500이 교차했다, 그들은 샘플링 시간 59 일 이전했다. 신선한 배설물과 쓰레기 샘플 (waterer / 급전선 사이에, waterer / 공급 라인 근처 패드를 냉각 근처, 배기 팬 근처) 집에서 네 가지 영역에서 회복하고, 각 영역에서 샘플 풀링 다섯을 포함했다 그 지역 내?...

Watch this Scientific Journal Video about A Hybrid DNA Extraction Method for the Qualitative and Quantitative Assessment of Bacterial Communities from Poultry Production Samples at JoVE.com

A Hybrid DNA Extraction Method for the Qualitative and Quantitative Assessment of Bacterial Communities from Poultry Production Samples

A novel semi-automated hybrid DNA extraction method for use with environmental poultry production samples was developed and demonstrated improvements over a common mechanical and enzymatic extraction method in terms of the quantitative and qualitative estimates of the total bacterial communities.

가금류 생산 샘플에서 세균 공동체의 정성 및 정량 평가를위한 하이브리드 DNA 추출 방법

The efficacy of DNA extraction protocols can be highly dependent upon both the type of sample being investigated and the types of downstream analyses ...

a-hybrid-dna-extraction-method-for-qualitative-quantitative

Research

JoVE Journal

Biology

14.4K 조회수.  USDA-Agricultural Research Service. A novel semi-automated hybrid DNA extraction method for use with environmental poultry production samples was developed and demonstrated improvements over a common mechanical and enzymatic extraction method in terms of the quantitative and qualitative estimates of the total bacterial communities. 

비디오: A Hybrid DNA Extraction Method for the Qualitative and Quantitative Assessment of Bacterial Communities from Poultry Production Samples

Purifying Plasmid DNA from Bacterial Colonies Using the Qiagen Miniprep Kit

Plasmid DNA purification from E. coli is a core technique for molecular cloning. Small scale purification (miniprep) from less than 5 ml of bacterial culture is a quick way for clone verification or DNA isolation, followed by further enzymatic reactions (polymerase chain reaction and restriction enzyme digestion). Here, we video-recorded the general procedures of miniprep through the QIAGEN's QIAprep 8 Miniprep Kit, aiming to introducing this highly efficient technique to the general beginners for molecular biology techniques. The whole procedure is based on alkaline lysis of E. coli cells followed by adsorption of DNA onto silica in the presence of high salt. It consists of three steps: 1) preparation and clearing of a bacterial lysate, 2) adsorption of DNA onto the QIAprep membrane, 3) washing and elution of plasmid DNA. All steps are performed without the use of phenol, chloroform, CsCl, ethidium bromide, and without alcohol precipitation. It usually takes less than 2 hours to finish the entire procedure.

Qiagen Miniprep 키트를 사용하여 세균의 플라스미드 식민지에서 DNA를 정화

Plasmid DNA purification from E. coli is a core technique for molecular cloning. Small scale purification (miniprep) from less than 5 ml of bacterial ...

연구

생물학

Use of Rotorod as a Method for the Qualitative Analysis of Walking in Rat

High speed videoanalysis of the details of movement can provide a source of information about qualitative aspects of walking movements. When walking on a rotorod, animals remain in approximately the same place making repetitive movements of stepping. Thus the task provides a rich source of information on the details of foot stepping movements. Subjects were hemi-Parkinson analogue rats, produced by injection of 6-hydroxydopamine (6-OHDA) into the right nigrostriatal bundle to deplete nigrostriatal dopamine (DA). The present report provides a video analysis illustration of animals previously were filmed from frontal, lateral, and posterior views as they walked (15). Rating scales and frame-by-frame replay of the video records of stepping behavior indicated that the hemi-Parkinson rats were chronically impaired in posture and limb use contralateral to the DA-depletion. The contralateral limbs participated less in initiating and sustaining propulsion than the ipsilateral limbs. These deficits secondary to unilateral DA-depletion show that the rotorod provides a use task for the analysis of stepping movements.

The rotorod test is used to assess motor status in the walking movement of hemi-Parkinson analogue rats.

쥐에서 도보의 질적 분석 방법으로 Rotorod의 사용

High speed videoanalysis of the details of movement can provide a source of information about qualitative aspects of walking movements. When walking on a ...

DNA Extraction from 0.22 &mu;M Sterivex Filters and Cesium Chloride Density Gradient Centrifugation

This method is used to extract high molecular weight genomic DNA from planktonic biomass concentrated on 0.22 &mu;M Sterivex filters that have been treated with storage/lysis buffer and archived at -80&deg;C, and to purify this DNA using a cesium chloride density gradient.  The protocol begins with two one-hour incubation steps to liberate DNA from cells and remove RNA.  Next, a series of Phenol:Chloroform and Chloroform extractions are performed followed by centrifugation to remove proteins and cell membrane components, collection of the aqueous DNA extract, and several buffer exchange steps to wash and concentrate the extract.  Part Five describes the optional purification via cesium chloride density gradient.  It is recommended to work with less than 15 samples at one time to avoid confusion and cut down protocol time. The total time required for this protocol depends on the number of samples to be extracted. For 10-15 samples and assuming the proper centrifugation equipment is available, this entire protocol should take 3 days. Make sure you have the hybridization ovens set to temperature at the outset of the process.

DNA Extraction from 0.22 &amp;mu;M Sterivex Filters and Cesium Chloride Density Gradient Centrifugation

We describe a method for extraction of high molecular weight genomic DNA from planktonic biomass concentrated on 0.22 &mu;m Sterivex filters, followed by cesium chloride density gradient centrifugation for purification.

0.22 μm의 Sterivex 필터 및 세슘 클로라이드 밀​​도 기울기 원심 분리 장치에서 DNA 추출

This method is used to extract high molecular weight genomic DNA from planktonic biomass concentrated on 0.22 &mu;M Sterivex filters that have been ...

Extraction of High Molecular Weight Genomic DNA from Soils and Sediments

The soil microbiome is a vast and relatively unexplored reservoir of genomic diversity and metabolic innovation that is intimately associated with nutrient and energy flow within terrestrial ecosystems. Cultivation-independent environmental genomic, also known as metagenomic, approaches promise unprecedented access to this genetic information with respect to pathway reconstruction and functional screening for high value therapeutic and biomass conversion processes. However, the soil microbiome still remains a challenge largely due to the difficulty in obtaining high molecular weight DNA of sufficient quality for large insert library production. Here we introduce a protocol for extracting high molecular weight, microbial community genomic DNA from soils and sediments. The quality of isolated genomic DNA is ideal for constructing large insert environmental genomic libraries for downstream sequencing and screening applications. 
The procedure starts with cell lysis. Cell walls and membranes of microbes are lysed by both mechanical (grinding) and chemical forces (&beta;-mercaptoethanol). Genomic DNA is then isolated using extraction buffer, chloroform-isoamyl alcohol and isopropyl alcohol. The buffers employed for the lysis and extraction steps include guanidine isothiocyanate and hexadecyltrimethylammonium bromide (CTAB) to preserve the integrity of the high molecular weight genomic DNA. Depending on your downstream application, the isolated genomic DNA can be further purified using cesium chloride (CsCl) gradient ultracentrifugation, which reduces impurities including humic acids. The first procedure, extraction, takes approximately 8 hours, excluding DNA quantification step. The CsCl gradient ultracentrifugation, is a two days process. During the entire procedure, genomic DNA should be treated gently to prevent shearing, avoid severe vortexing, and repetitive harsh pipetting.

A methodology to isolate high molecular weight and high quality genomic DNA from soil microbial community is described.

소일스 및 세디먼츠에서 높은 분자량의 게놈의 DNA의 추출

The soil microbiome is a vast and relatively unexplored reservoir of genomic diversity and metabolic innovation that is intimately associated with ...

DNA Extraction from Paraffin Embedded Material for Genetic and Epigenetic Analyses

Disease development and progression are characterized by frequent genetic and epigenetic aberrations including chromosomal rearrangements, copy number gains and losses and DNA methylation. Advances in high-throughput, genome-wide profiling technologies, such as microarrays, have significantly improved our ability to identify and detect these specific alterations. However as technology continues to improve, a limiting factor remains sample quality and availability. Furthermore, follow-up clinical information and disease outcome are often collected years after the initial specimen collection. Specimens, typically formalin-fixed and paraffin embedded (FFPE), are stored in hospital archives for years to decades. DNA can be efficiently and effectively recovered from paraffin-embedded specimens if the appropriate method of extraction is applied. High quality DNA extracted from properly preserved and stored specimens can support quantitative assays for comparisons of normal and diseased tissues and generation of genetic and epigenetic signatures 1. To extract DNA from paraffin-embedded samples, tissue cores or microdissected tissue are subjected to xylene treatment, which dissolves the paraffin from the tissue, and then rehydrated using a series of ethanol washes. Proteins and harmful enzymes such as nucleases are subsequently digested by proteinase K. The addition of lysis buffer, which contains denaturing agents such as sodium dodecyl sulfate (SDS), facilitates digestion 2. Nucleic acids are purified from the tissue lysate using buffer-saturated phenol and high speed centrifugation which generates a biphasic solution. DNA and RNA remain in the upper aqueous phase, while proteins, lipids and polysaccharides are sequestered in the inter- and organic-phases respectively. Retention of the aqueous phase and repeated phenol extractions generates a clean sample. Following phenol extractions, RNase A is added to eliminate contaminating RNA. Additional phenol extractions following incubation with RNase A are used to remove any remaining enzyme. The addition of sodium acetate and isopropanol precipitates DNA, and high speed centrifugation is used to pellet the DNA and facilitate isopropanol removal. Excess salts carried over from precipitation can interfere with subsequent enzymatic assays, but can be removed from the DNA by washing with 70% ethanol, followed by centrifugation to re-pellet the DNA 3. DNA is re-suspended in distilled water or the buffer of choice, quantified and stored at -20&deg;C. Purified DNA can subsequently be used in downstream applications which include, but are not limited to, PCR, array comparative genomic hybridization 4 (array CGH), methylated DNA Immunoprecipitation (MeDIP) and sequencing, allowing for an integrative analysis of tissue/tumor samples.

This video demonstrates the protocol for DNA extraction from formalin-fixed paraffin-embedded material. This is a multi-day procedure in which tissue sections are deparaffinized with xylene, rehydrated with ethanol and treated with proteinase K to purify and isolate DNA for subsequent gene-specific or genome-wide analysis.

유전과 Epigenetic 분석을위한 파라핀 임베디드 재료에서 DNA 추출

Disease development and progression are characterized by frequent genetic and epigenetic aberrations including chromosomal rearrangements, copy number ...

Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization

There is a growing appreciation for the role of microbial communities as critical modulators of human health and disease. High throughput sequencing technologies have allowed for the rapid and efficient characterization of bacterial communities using 16S rRNA gene sequencing from a variety of sources. Although readily available tools for 16S rRNA sequence analysis have standardized computational workflows, sample processing for DNA extraction remains a continued source of variability across studies. Here we describe an efficient, robust, and cost effective method for extracting nucleic acid from swabs. We also delineate downstream methods for 16S rRNA gene sequencing, including generation of sequencing libraries, data quality control, and sequence analysis. The workflow can accommodate multiple samples types, including stool and swabs collected from a variety of anatomical locations and host species. Additionally, recovered DNA and RNA can be separated and used for other applications, including whole genome sequencing or RNA-seq. The method described allows for a common processing approach for multiple sample types and accommodates downstream analysis of genomic, metagenomic and transcriptional information.

We describe an efficient, robust, and cost effective method for extracting nucleic acid from swabs for characterization of bacterial communities using 16S rRNA gene amplicon sequencing. The method allows for a common processing approach for multiple sample types and accommodates a number of downstream analytic processes.

세균 커뮤니티 특성화에 대한 효율적인 핵산 추출 및 16S rRNA의 유전자 시퀀싱

There is a growing appreciation for the role of microbial communities as critical modulators of human health and disease. High throughput sequencing ...

Filtration Isolation of Nucleic Acids:  A Simple and Rapid DNA Extraction Method

FINA, filtration isolation of nucleic acids, is a novel extraction method which utilizes vertical filtration via a separation membrane and absorbent pad to extract cellular DNA from whole blood in less than 2 min. The blood specimen is treated with detergent, mixed briefly and applied by pipet to the separation membrane. The lysate wicks into the blotting pad due to capillary action, capturing the genomic DNA on the surface of the separation membrane. The extracted DNA is retained on the membrane during a simple wash step wherein PCR inhibitors are wicked into the absorbent blotting pad. The membrane containing the entrapped DNA is then added to the PCR reaction without further purification. This simple method does not require laboratory equipment and can be easily implemented with inexpensive laboratory supplies. Here we describe a protocol for highly sensitive detection and quantitation of HIV-1 proviral DNA from 100 &#181;l whole blood as a model for early infant diagnosis of HIV that could readily be adapted to other genetic targets.

We describe here a simple and rapid paper-based DNA extraction method of HIV proviral DNA from whole blood detected by quantitative PCR. This protocol can be extended for use in detecting other genetic markers or using alternative amplification methods.

핵산의 여과 분리 : 간단하고 신속한 DNA 추출 방법

FINA, filtration isolation of nucleic acids, is a novel extraction method which utilizes vertical filtration via a separation membrane and absorbent pad ...

Hybrid-Cut: An Improved Sectioning Method for Recalcitrant Plant Tissue Samples

Maintaining plant section integrity is essential for studying detailed anatomical structures at the cellular, tissue, or even organ level. However, some plant cells have rigid cell walls, tough fibers and crystals (calcium oxalate, silica, etc.), and high water content that often disrupt tissue integrity during plant tissue sectioning.
This study establishes a simple Hybrid-Cut tissue sectioning method. This protocol modifies a paraffin-based sectioning technique and improves the integrity of tissue sections from different plants. Plant tissues were embedded in paraffin before sectioning in a cryostat at -16 &#176;C. Sectioning under low temperature hardened the paraffin blocks, reduced tearing and scratching, and improved tissue integrity significantly. This protocol was successfully applied to calcium oxalate-rich Phalaenopsis orchid tissues as well as recalcitrant tissues such as reproductive organs and leaves of rice, maize, and wheat. In addition, the high quality of tissue sections from Hybrid-Cut could be used in combination with in situ hybridization (ISH) to provide spatial expression patterns of genes of interest. In conclusion, this protocol is particularly useful for recalcitrant plant tissue containing high crystal or silica content. Good quality tissue sections enable morphological and other biological studies.

This protocol describes a simple Hybrid-Cut tissue sectioning method that is useful for recalcitrant plant tissues. Good quality tissue sections enable anatomical studies and other biological studies including in situ hybridization (ISH).

하이브리드 컷 : 난 분해성 식물 조직 샘플에 대한 개선 단면 방법

Maintaining plant section integrity is essential for studying detailed anatomical structures at the cellular, tissue, or even organ level. However, some ...

Quasi-metagenomic Analysis of Salmonella from Food and Environmental Samples

Quasi-metagenomics sequencing refers to the sequencing-based analysis of modified microbiomes of food and environmental samples. In this protocol, microbiome modification is designed to concentrate genomic DNA of a target foodborne pathogen contaminant to facilitate the detection and subtyping of the pathogen in a single workflow. Here, we explain and demonstrate the sample preparation steps for the quasi-metagenomics analysis of Salmonella enterica from representative food and environmental samples including alfalfa sprouts, ground black pepper, ground beef, chicken breast and environmental swabs. Samples are first subjected to the culture enrichment of Salmonella for a shortened and adjustable duration (4&#8211;24 h). Salmonella cells are then selectively captured from the enrichment culture by immunomagnetic separation (IMS). Finally, multiple displacement amplification (MDA) is performed to amplify DNA from IMS-captured cells. The DNA output of this protocol can be sequenced by high throughput sequencing platforms. An optional quantitative PCR analysis can be performed to replace sequencing for Salmonella detection or assess the concentration of Salmonella DNA before sequencing.

Quasi-metagenomic Analysis of Salmonella from Food and Environmental Samples

Here, we present a protocol to prepare DNA samples from food and environmental microbiomes for concerted detection and subtyping of Salmonella through quasimetagenomic sequencing. The combined use of culture enrichment, immunomagnetic separation (IMS), and multiple displacement amplification (MDA) allows effective concentration of Salmonella genomic DNA from food and environmental samples.&#160;

음식과 환경 샘플에서 살 모 넬 라 의 준 metagenomic 분석

Quasi-metagenomics sequencing refers to the sequencing-based analysis of modified microbiomes of food and environmental samples. In this protocol, ...

녹농균 분리체(Pseudomonas aeruginosa Isolates)의 Siderophore 생산 평가

Qualitative and Quantitative Analysis of Siderophore Production from Pseudomonas aeruginosa

Pseudomonas aeruginosa (P. aeruginosa) is known for its production of a diverse range of virulence factors to establish infections in the host. One such mechanism is the scavenging of iron through siderophore production. P. aeruginosa produces two different siderophores: pyochelin, which has lower iron-chelating affinity, and pyoverdine, which has higher iron-chelating affinity. This report demonstrates that pyoverdine can be directly quantified from bacterial supernatants, while pyochelin needs to be extracted from supernatants before quantification.
The primary method for qualitatively analyzing siderophore production is the Chrome Azurol Sulfonate (CAS) agar plate assay. In this assay, the release of CAS dye from the Fe3+-Dye complex leads to a color change from blue to orange, indicating siderophore production. For the quantification of total siderophores, bacterial supernatants were mixed in equal proportions with CAS dye in a microtiter plate, followed by spectrophotometric analysis at 630 nm. Pyoverdine was directly quantified from the bacterial supernatant by mixing it in equal proportions with 50 mM Tris-HCl, followed by spectrophotometric analysis. A peak at 380 nm confirmed the presence of pyoverdine. As for Pyochelin, direct quantification from the bacterial supernatant was not possible, so it had to be extracted first. Subsequent spectrophotometric analysis revealed the presence of pyochelin, with a peak at 313 nm.

저자 스포트라이트: 감염 통제를 위한 Siderophores 및 Pyochelin 정량화 

This protocol provides both qualitative and quantitative analyses of total siderophores, pyoverdine, and pyochelin from Pseudomonas aeruginosa.

녹농균(Pseudomonas aeruginosa)의 Siderophore 생산에 대한 정성적 및 정량적 분석

Pseudomonas aeruginosa (P. aeruginosa) is known for its production of a diverse range of virulence factors to establish infections in the host. One such ...