この研究は 、中国国家自然科学基金(82230080)の主要プロジェクトであるNational Science Fund for Distinguished Young Scholars(82025024)の支援を受けました。中国の国家重点研究開発プログラム(2021YFA1300604);中国国家自然科学基金会(81871735、82272438、82002245)広東省著名な若手学者のための広東省自然科学基金(2023B1515020058); 広東省自然科学財団(2021A1515011639); 中国山東省自然科学基金会の主要国家基礎研究開発プログラム(ZR2020ZD11) ポスドク科学財団(2022M720059);南方医科大学南方病院の優れた青少年育成スキーム(2022J001)。

微生物叢マルチオミクスのための細菌細胞外小胞の単離の強化

<ol>
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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=Extracellular+vesicles+derived+from+gut+microbiota,+especially+Akkermansia+muciniphila,+protect+the+progression+of+dextran+sulfate+sodium-induced+colitis.">Extracellular vesicles derived from gut microbiota, especially Akkermansia muciniphila, protect the progression of dextran sulfate sodium-induced colitis.</a> PloS one. 8 (10), 76520 (2013).</li><li>Simonsen, J. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=What+are+we+looking+at?+Extracellular+vesicles,+lipoproteins,+or+both.">What are we looking at? Extracellular vesicles, lipoproteins, or both.</a> Circulation Research. 121 (8), 920-922 (2017).</li><li>Correll, V. L., 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=Optimization+of+small+extracellular+vesicle+isolation+from+expressed+prostatic+secretions+in+urine+for+in-depth+proteomic+analysis.">Optimization of small extracellular vesicle isolation from expressed prostatic secretions in urine for in-depth proteomic analysis.</a> Journal of Extracellular Vesicles. 11 (2), 12184 (2022).</li><li>Liang, 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=Gut+bacterial+extracellular+vesicles:+important+players+in+regulating+intestinal+microenvironment.">Gut bacterial extracellular vesicles: important players in regulating intestinal microenvironment.</a> Gut Microbes. 14 (1), 2134689 (2022).</li><li>Alberti, 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=Extracellular+vesicles+derived+from+gut+microbiota+in+inflammatory+bowel+disease+and+colorectal+cancer.">Extracellular vesicles derived from gut microbiota in inflammatory bowel disease and colorectal cancer.</a> Biomedical papers of the Medical Faculty of the University Palacky, Olomouc, Czech Republic. 165 (3), 233-240 (2021).</li><li>D&#237;ez-Sainz, E., Milagro, F. I., Riezu-Boj, J. I., Lorente-Cebri&#225;n, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effects+of+gut+microbiota-derived+extracellular+vesicles+on+obesity+and+diabetes+and+their+potential+modulation+through+diet.">Effects of gut microbiota-derived extracellular vesicles on obesity and diabetes and their potential modulation through diet.</a> Journal of Physiology and Biochemistry. 78 (2), 485-499 (2022).</li><li>Lajqi, T., 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=Gut+microbiota-derived+small+extracellular+vesicles+endorse+memory-like+inflammatory+responses+in+murine+neutrophils.">Gut microbiota-derived small extracellular vesicles endorse memory-like inflammatory responses in murine neutrophils.</a> Biomedicines. 10 (2), 442 (2022).</li><li>Lee, K. E., 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+extracellular+vesicle+of+gut+microbial+Paenalcaligenes+hominis+is+a+risk+factor+for+vagus+nerve-mediated+cognitive+impairment.">The extracellular vesicle of gut microbial Paenalcaligenes hominis is a risk factor for vagus nerve-mediated cognitive impairment.</a> Microbiome. 8 (1), 107 (2020).</li><li>Villard, A., Boursier, J., Andriantsitohaina, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bacterial+and+eukaryotic+extracellular+vesicles+and+nonalcoholic+fatty+liver+disease:+new+players+in+the+gut-liver+axis.">Bacterial and eukaryotic extracellular vesicles and nonalcoholic fatty liver disease: new players in the gut-liver axis.</a> American Journal of Physiology-Gastrointestinal and Liver Physiology. 320 (4), G485-G495 (2021).</li><li>Wei, 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=Outer+membrane+vesicles+enhance+tau+phosphorylation+and+contribute+to+cognitive+impairment.">Outer membrane vesicles enhance tau phosphorylation and contribute to cognitive impairment.</a> Journal of Cellular Physiology. 235 (5), 4843-4855 (2020).</li><li>Bitto, N. 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R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Production,+isolation,+and+characterization+of+bioengineered+bacterial+extracellular+membrane+vesicles+derived+from+Bacteroides+thetaiotaomicron+and+their+use+in+vaccine+development.">Production, isolation, and characterization of bioengineered bacterial extracellular membrane vesicles derived from Bacteroides thetaiotaomicron and their use in vaccine development.</a> Methods in Molecular Biology. 2414, 171-190 (2022).</li><li>Zhang, Q., Jeppesen, D. K., Higginbotham, J. N., Franklin, J. L., Coffey, R. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comprehensive+isolation+of+extracellular+vesicles+and+nanoparticles.">Comprehensive isolation of extracellular vesicles and nanoparticles.</a> Nature Protocols. 18 (5), 1462-1487 (2023).</li><li>Iwai, K., Minamisawa, T., Suga, K., Yajima, Y., Shiba, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolation+of+human+salivary+extracellular+vesicles+by+iodixanol+density+gradient+ultracentrifugation+and+their+characterizations.">Isolation of human salivary extracellular vesicles by iodixanol density gradient ultracentrifugation and their characterizations.</a> Journal of Extracellular Vesicles. 5, 30829 (2016).</li><li>Vandeputte, D., 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=Stool+consistency+is+strongly+associated+with+gut+microbiota+richness+and+composition,+enterotypes+and+bacterial+growth+rates.">Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates.</a> Gut. 65 (1), 57-62 (2016).</li><li>Wen, 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=Bacterial+extracellular+vesicles:+A+position+paper+by+the+Microbial+Vesicles+Task+Force+of+the+Chinese+Society+of+Extracellular+Vesicles.">Bacterial extracellular vesicles: A position paper by the Microbial Vesicles Task Force of the Chinese Society of Extracellular Vesicles.</a> Interdisciplinary Medicine. 1, 12046 (2023).</li></ol>

著者は、相反する利害関係がないことを宣言します。

細菌の細胞外小胞(BEV)は、細菌から分泌される脂質二重層ナノ粒子であり、タンパク質、脂質、核酸、その他の生理活性分子を豊富に含み、細菌の機能的効果の媒介に寄与する20。腸に由来するBEVは、炎症性腸疾患、クローン病、大腸がんなどの疾患の発症に関与し、一般的な代謝に影響を与え、認知機能障害を媒介することが確認されています4,16,17,20,21,2...

腸は、人体で最も豊富な微生物群集を持つ器官として広く認識されており、細菌の90%以上がコロニー形成と増殖に関与しています1,2。腸内細菌叢は腸内微小環境を調節し、同時に主に腸管関門の障害を介して遠隔臓器の機能障害と相互作用することが広範な証拠によって実証されています3,4。腸内細菌叢の不均衡と炎症性腸疾患(IBD)の進行5,6、および腸脳軸を介した認知障害との相関関係を示す証拠が増えています5,6,7,8。細菌によって産生される細菌の細胞外小胞(BEV)は、これらの病理学的プロセスにおいて重要な役割を果たします。
BEVは、直径20〜400nmの細菌誘導体をカプセル化するナノスケールの粒子です。それらは、バクテリアとその宿主生物との間の相互作用を促進することが実証されています9,10。これらの粒子は目に見えないにもかかわらず、診断バイオマーカー、治療標的、薬物送達媒体として幅広い用途が期待されているため、研究者からの注目が高まっています11。主に腸内細菌を原料とするヒトの糞便は、BEV研究の生体試料としてよく使用され、水、細菌、脂質、タンパク質、未消化の食物残渣、剥離した上皮細胞などが複雑に混ざり合っています。複雑な糞便組成は、BEVの分離と純度に課題をもたらし、BEVの包括的、客観的、かつ現実的な分析を妨げています。したがって、汚染されたコンポーネントからの干渉を最小限に抑え、BEVの歩留まりを向上させるための効果的な戦略が、早急な対応を必要とする重要な問題として浮上しています。
既存の単離戦略は、超高速遠心分離(UC)、密度勾配遠心分離(DGC)、サイズ排除クロマトグラフィー(SEC)などの技術に大きく依存しています12,13,14,15,16,17。現在、DGCはBEV分離の分野で最も広く適用されている方法の1つであり、サンプルの初期ローディング位置によって決定される「トップダウン」と「ボトムアップ」の2つの沈降フローティングモードを包含しています。これらの方法論は、サイズと密度の格差に基づいて細胞外小胞(EV)を他の成分と区別し、さまざまな純度と回収率を生み出します。これまでの研究では、血液中のリポタンパク質18や尿中のTamm-Horsfallタンパク質19など、体液サンプル中の可溶性タンパク質からEVを適切に分離するには、シングルアプローチ戦略では不十分であることが示されています。さらに、真核生物の細胞外小胞(EEV)のサイズ分布はBEVのサイズ分布と重複することが多いため、BEVの収量を最適化するには、さらなる方法論的強化が必要です。したがって、BEVの研究を進めるには、効果的な分離および精製方法の開発にかかっています。特に、Tulkens et al 15 は、糞便 BEV を EEV から分離するために直交生物物理学的戦略を採用しており、ボトムアップ DGC モードの遠心分離時間は最大18 時間でした。対照的に、この試験では 7 時間に短縮され、グラジエント超遠心分離時間が大幅に短縮され、プロセスが簡素化されました。
本研究では、低速から超高速まで、さまざまな異なる遠心分離速度でBEVを濃縮した後、最適化された緩衝条件下で、2つのDGCモードを用いて糞便BEVを分離および精製しました。形態、粒子径、および濃度に基づく評価は、この強化された分析法による称賛に値する性能を示しました。この研究は、将来の研究の基盤となり、その応用範囲をより広い領域に拡大し、人体におけるBEVの不均一性に関する洞察を提供する可能性があります。また、BEVの分離・分析技術の標準化にも貢献します。

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>1 % (w/v) glutaraldehyde (prepared from 2.5 % stock solution in deionized water)</td>
			<td>ACMEC</td>
			<td>AP1126</td>
			<td>Morphological observation for BEVs using TEM at Step 8.3.3</td>
		</tr>
		<tr>
			<td>1 % (w/v) methylcellulose (prepared from original powder in deionized water)</td>
			<td>Sigma-Aldrich</td>
			<td>M7027</td>
			<td>Morphological observation for BEVs using TEM at Step 8.3.6</td>
		</tr>
		<tr>
			<td>1.5 % (w/v) uranyl acetate (prepared from original powder in deionized water)</td>
			<td>Polysciences</td>
			<td>21447-25</td>
			<td>Morphological observation for BEVs using TEM at Step 8.3.5</td>
		</tr>
		<tr>
			<td>1000 &#956;L, 200 &#956;L, 10 &#956;L Pipette</td>
			<td>KIRGEN</td>
			<td>KG1313, KG1212, KG1011</td>
			<td>Transfer the solution</td>
		</tr>
		<tr>
			<td>5 % (w/v) bovine serum albumin solution (prepared from the original powder in TBST buffer)</td>
			<td>Fdbio science</td>
			<td>FD0030</td>
			<td>Used in western blotting for blocking at Step 8.5.6</td>
		</tr>
		<tr>
			<td>5 &#215; loading buffer</td>
			<td>Fdbio science</td>
			<td>FD006</td>
			<td>Used in western blotting and Coomassie brilliant blue stain at Step 8.5.1</td>
		</tr>
		<tr>
			<td>75 % (v/v) alcohol</td>
			<td>LIRCON</td>
			<td>LIRCON-500 mL</td>
			<td>Surface disinfection</td>
		</tr>
		<tr>
			<td>96-well plate</td>
			<td>Rar</td>
			<td>A8096</td>
			<td>Measure the absorbance values&#160;</td>
		</tr>
		<tr>
			<td>Anti-Calnexin antibody</td>
			<td>Abcam</td>
			<td>ab92573</td>
			<td>Western blotting (Primary Antibody)</td>
		</tr>
		<tr>
			<td>Anti-CD63 antibody</td>
			<td>Abcam</td>
			<td>ab134045</td>
			<td>Western blotting (Primary Antibody)</td>
		</tr>
		<tr>
			<td>Anti-CD9 antibody</td>
			<td>Abcam</td>
			<td>ab236630</td>
			<td>Western blotting (Primary Antibody)</td>
		</tr>
		<tr>
			<td>Anti-Flagellin antibody</td>
			<td>Sino Biological</td>
			<td>40067-MM06</td>
			<td>Western blotting (Primary Antibody)</td>
		</tr>
		<tr>
			<td>Anti-Integrin beta 1 antibody</td>
			<td>Abcam</td>
			<td>ab30394</td>
			<td>Western blotting (Primary Antibody)</td>
		</tr>
		<tr>
			<td>Anti-LPS antibody</td>
			<td>Thermo Fisher</td>
			<td>MA1-83152</td>
			<td>Western blotting (Primary Antibody)</td>
		</tr>
		<tr>
			<td>Anti-LTA antibody</td>
			<td>Thermo Fisher&#160;</td>
			<td>MA1-7402</td>
			<td>Western blotting (Primary Antibody)</td>
		</tr>
		<tr>
			<td>Anti-OmpA antibody</td>
			<td>CUSABIO</td>
			<td>CSB-PA359226ZA01EOD, https://www.cusabio.com/</td>
			<td>Western blotting (Primary Antibody)</td>
		</tr>
		<tr>
			<td>Anti-Syntenin antibody</td>
			<td>Abcam</td>
			<td>ab133267</td>
			<td>Western blotting (Primary Antibody)</td>
		</tr>
		<tr>
			<td>Anti-TSG101 antibody</td>
			<td>Abcam</td>
			<td>ab125011</td>
			<td>Western blotting (Primary Antibody)</td>
		</tr>
		<tr>
			<td>Autoclave</td>
			<td>ZEALWAY</td>
			<td>GR110DP</td>
			<td>Sterilization for supplies and mediums used in the experiment</td>
		</tr>
		<tr>
			<td>Balance</td>
			<td>Mettler Toledo</td>
			<td>AL104</td>
			<td>Balance the tube sample-loaded with PBS</td>
		</tr>
		<tr>
			<td>Bicinchoninic acid assay&#160;</td>
			<td>Fdbio science</td>
			<td>FD2001</td>
			<td>Measure protein content of BEVs at Step 8.2</td>
		</tr>
		<tr>
			<td>BioRender</td>
			<td>BioRender</td>
			<td>https://app.biorender.com</td>
			<td>Make the schematic workflow of BEVs isolation and purification showed in Figure 1</td>
		</tr>
		<tr>
			<td>Biosafety cabinet</td>
			<td>Haier</td>
			<td>HR1200- II B2</td>
			<td>Peform the procedures about feces sample handling</td>
		</tr>
		<tr>
			<td>Centrifuge 5810 R; Rotor F-34-6-38</td>
			<td>Eppendorf</td>
			<td>5805000092; 5804727002, adapter: 5804774000</td>
			<td>Preprocess for BEVs (Step 3)</td>
		</tr>
		<tr>
			<td>Chemiluminescence Apparatus</td>
			<td>BIO-OI</td>
			<td>OI600SE-MF</td>
			<td>Used in western blotting for signal detection at Step 8.5.12</td>
		</tr>
		<tr>
			<td>Cytation 5</td>
			<td>BioTek</td>
			<td>F01</td>
			<td>Microplate detector for measuring the absorbance (Step 8.1) and fluorescence (Figure 6) values&#160;</td>
		</tr>
		<tr>
			<td>Dil-labled low density lipoprotein</td>
			<td>ACMEC</td>
			<td>AC12038</td>
			<td>Definition of distribution of interfering components&#160;</td>
		</tr>
		<tr>
			<td>Electrophoresis equipment</td>
			<td>Bio-rad</td>
			<td>1658033</td>
			<td>Used in western blotting for protein separation and transfer at Step 8.5.2, 8.5.3, 8.5.5</td>
		</tr>
		<tr>
			<td>Enhanced Chemiluminescence kit HRP&#160;</td>
			<td>Fdbio science</td>
			<td>FD8020</td>
			<td>Used in western blotting for signal detection at Step 8.5.12</td>
		</tr>
		<tr>
			<td>Escherichia coli&#160;</td>
			<td>American Type Culture Collection</td>
			<td>ATCC8739</td>
			<td>Isolate BEVs as a positive control. Protocol: Dissolve 25 g of the LB powder in 1 L deionized water, and autoclave. Transfer the 800 &#956;L of preserved Escherichia coli into the medium. Cultivate at 37 &#176;C in the incubator shaker. Then centrifuge at 3, 000 &#215; g for 20 min at 4 &#176;C, 12, 000 &#215; g for 30 min at 4 &#176;C, filter the supernatant through 0.22 &#956;m membrane, and perform ultra-speed centrifugation at 160, 000 &#215; g for 70 min at 4 &#176;C. Pellet defined as crude BEVs from Escherichia coli was suspended in 1.2 mL PBS (Step 3, 4).&#160;&#160;&#160;&#160;</td>
		</tr>
		<tr>
			<td>Falcon tubes 50 mL</td>
			<td>KIRGEN</td>
			<td>KG2811</td>
			<td>Preprocess for BEVs (Step 3)</td>
		</tr>
		<tr>
			<td>Feto Protein Staining Buffer</td>
			<td>Absci</td>
			<td>ab.001.50</td>
			<td>Coomassie brilliant blue staining at Step 8.5.4</td>
		</tr>
		<tr>
			<td>Filter paper</td>
			<td>Biosharp</td>
			<td>BS-TFP-070B</td>
			<td>Morphological observation for BEVs using TEM at Step 8.3 (Blotting the solution)</td>
		</tr>
		<tr>
			<td>Formvar/Carbon supported copper grids&#160;</td>
			<td>Sigma-Aldrich</td>
			<td>TEM-FCF200CU50</td>
			<td>Morphological observation for BEVs using TEM at Step 8.3</td>
		</tr>
		<tr>
			<td>HEPES powder</td>
			<td>Meilunbio</td>
			<td>MB6078</td>
			<td>Prepare iodixanol buffers with different concentrations for density gradient centrifugation</td>
		</tr>
		<tr>
			<td>HRP AffiniPure Goat Anti-Mouse IgG (H+L)</td>
			<td>Fdbio science</td>
			<td>FDM007</td>
			<td>Western blotting (Secondary Antibody)</td>
		</tr>
		<tr>
			<td>HRP AffiniPure Goat Anti-Rabbit IgG (H+L)</td>
			<td>Fdbio science</td>
			<td>FDR007</td>
			<td>Western blotting (Secondary Antibody)</td>
		</tr>
		<tr>
			<td>Incubator shaker</td>
			<td>Qiangwen</td>
			<td>DHZ-L</td>
			<td>Cultivate Escherichia coli&#160;</td>
		</tr>
		<tr>
			<td>Kimwipes&#8482; Delicate Task Wipes</td>
			<td>Kimtech Science</td>
			<td>34155</td>
			<td>Wipe the inner wall of the ultracentrifuge tube at Step 4.15</td>
		</tr>
		<tr>
			<td>LB broth</td>
			<td>Hopebio</td>
			<td>HB0128</td>
			<td>Cultivate Escherichia coli&#160;</td>
		</tr>
		<tr>
			<td>Low temperature freezer (-80 &#176;C)</td>
			<td>Haier</td>
			<td>DW-86L338J</td>
			<td>Store the samples</td>
		</tr>
		<tr>
			<td>Methanol</td>
			<td>Alalddin</td>
			<td>M116118</td>
			<td>Used in western blotting for activating PVDF membrane at Step 8.5.5</td>
		</tr>
		<tr>
			<td>Micro tubes 1.5 mL</td>
			<td>KIRGEN</td>
			<td>KG2211</td>
			<td>Recover fractions after density gradient centrifugation</td>
		</tr>
		<tr>
			<td>Micro tubes 2 mL</td>
			<td>KIRGEN</td>
			<td>KG2911</td>
			<td>Recover fractions after density gradient centrifugation</td>
		</tr>
		<tr>
			<td>Micro tubes 5 mL</td>
			<td>BBI</td>
			<td>F610888-0001</td>
			<td>Recover fractions after density gradient centrifugation</td>
		</tr>
		<tr>
			<td>Microplate reader&#160;</td>
			<td>Thermo Fisher&#160;</td>
			<td>Multiskan MK3</td>
			<td>Measure protein content of BEVs at Step 8.2</td>
		</tr>
		<tr>
			<td>Millipore filter 0.22 &#956;m</td>
			<td>Merck millipore</td>
			<td>SLGP033RB</td>
			<td>Filtration sterilization; Material: polyethersulfone, PES</td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td>GHTECH</td>
			<td>1.01307.040</td>
			<td>Density gradient centrifugation solution</td>
		</tr>
		<tr>
			<td>NaOH</td>
			<td>GHTECH</td>
			<td>1.01394.068</td>
			<td>Density gradient centrifugation solution (pH adjustment)</td>
		</tr>
		<tr>
			<td>Optima&#8482; XPN-100</td>
			<td>Beckman Coulter</td>
			<td>A94469</td>
			<td>Ultracentrifugation for BEVs isolation at Step 4, 7</td>
		</tr>
		<tr>
			<td>OptiPrep&#8482;</td>
			<td>Serumwerk Bernburg AG</td>
			<td>1893</td>
			<td>Density gradient centrifugation stock solution</td>
		</tr>
		<tr>
			<td>Orbital Shaker</td>
			<td>Youning</td>
			<td>CS-100</td>
			<td>Dissolve feces at Step 2</td>
		</tr>
		<tr>
			<td>Phosphate buffered saline</td>
			<td>Procell</td>
			<td>PB180327</td>
			<td>Dissolve feces at Step 2</td>
		</tr>
		<tr>
			<td>Pipettor</td>
			<td>Eppendorf</td>
			<td>3120000267, 3120000259</td>
			<td>Transfer the solution</td>
		</tr>
		<tr>
			<td>Plastic pasteur pipette</td>
			<td>ABCbio</td>
			<td>ABC217003-4</td>
			<td>Remove supernatant in preprocessing at Step 3.4</td>
		</tr>
		<tr>
			<td>Polyvinylidene difluoride (PVDF) membranes</td>
			<td>Millipore</td>
			<td>ISEQ00010, IPVH00010</td>
			<td>Used in western blotting for protein transfer at Step 8.5.5</td>
		</tr>
		<tr>
			<td>Prefabricated polyacrylamide gel, 4&#8211;20% 15 Wells</td>
			<td>ACE</td>
			<td>F15420Gel</td>
			<td>Used in western blotting for protein separation at Step 8.5.2, 8.5.3</td>
		</tr>
		<tr>
			<td>Primary antibody diluent</td>
			<td>Fdbio science</td>
			<td>FD0040</td>
			<td>Used in western blotting at Step 8.5.8</td>
		</tr>
		<tr>
			<td>Protein ladder</td>
			<td>Fdbio science</td>
			<td>FD0672</td>
			<td>Used in western blotting and Coomassie brilliant blue stain at Step 8.5</td>
		</tr>
		<tr>
			<td>Rapid protein blotting solution</td>
			<td>UBIO</td>
			<td>UW0500</td>
			<td>Used in western blotting for protein transfer at Step 8.5.5</td>
		</tr>
		<tr>
			<td>Rotor SW 32 Ti Swinging-Bucket Rotor</td>
			<td>Beckman Coulter</td>
			<td>369650</td>
			<td>Ultracentrifugation for BEVs isolation at Step 4, 7</td>
		</tr>
		<tr>
			<td>Syringe 20 mL, 50 mL&#160;</td>
			<td>Jetway</td>
			<td>ZSQ-20ML, YCXWJZSQ-50 mL</td>
			<td>Transfer buffers amd remove supernatant in preprocessing</td>
		</tr>
		<tr>
			<td>TBS powder</td>
			<td>Fdbio science</td>
			<td>FD1021</td>
			<td>Used in western blotting at Step 8.5</td>
		</tr>
		<tr>
			<td>Transmission electron microscope (TEM)</td>
			<td>Hitachi&#160;</td>
			<td>H-7650</td>
			<td>Morphological observation for BEVs at Step 8.3</td>
		</tr>
		<tr>
			<td>Tween-20</td>
			<td>Fdbio science</td>
			<td>FD0020</td>
			<td>Used in western blotting at Step 8.5</td>
		</tr>
		<tr>
			<td>Ultracentrifuge tube</td>
			<td>Beckman</td>
			<td>326823, 355642</td>
			<td>Ultracentrifugation for BEVs isolation at Step 4, 7</td>
		</tr>
		<tr>
			<td>Ultra-clean bench</td>
			<td>AIRTECH</td>
			<td>SW-CJ-2FD</td>
			<td>Peform the procedures about liquid handling</td>
		</tr>
		<tr>
			<td>Water bath</td>
			<td>Bluepard</td>
			<td>CU600</td>
			<td>Used for measuring protein content of BEVs at Step 8.2.5</td>
		</tr>
		<tr>
			<td>ZetaView</td>
			<td>Particle Metrix</td>
			<td>S/N 21-734, Software ZetaView (version 8.05.14 SP7)</td>
			<td>Nanoparticle tracking analysis (NTA) for measuring the particle size and concentrarion of BEVs at Step 8.4</td>
		</tr>
	</tbody>
</table>

isolation and purification of bacterial extracellular vesicles from human feces using density gradient centrifugation

細菌細胞外小胞(BEV)は、細菌由来のナノ小胞で、細菌間および細菌と宿主のコミュニケーションにおいて積極的な役割を果たし、親細菌から受け継いだタンパク質、脂質、核酸などの生理活性分子を輸送します。腸内細菌叢に由来するBEVは、消化管内で作用し、遠隔地の臓器に到達する可能性があるため、生理学や病理学に大きな影響を与えます。ヒトの糞便に由来するBEVの種類、量、役割を探る理論的研究は、腸内細菌叢からのBEVの分泌と機能を理解する上で非常に重要です。これらの調査では、BEVの分離と精製に関する現在の戦略の改善も必要になります。
この研究では、トップダウンとボトムアップの2つの密度勾配遠心分離(DGC)モードを確立することにより、BEVの分離および精製プロセスを最適化しました。BEVの濃縮分布は、フラクション6〜8(F6-F8)で決定されました。このアプローチの有効性は、粒子の形態、サイズ、濃度、およびタンパク質含有量に基づいて評価されました。粒子およびタンパク質の回収率を計算し、特定のマーカーの存在を分析して、2 つの DGC モードの回収率と純度を比較しました。その結果、トップダウン遠心分離モードの方が汚染レベルが低く、ボトムアップモードと同等の回収率と純度を達成していることが示されました。7時間の遠心分離時間は、糞便BEV濃度108/mgを達成するのに十分でした。
糞便とは別に、この方法は、成分と粘度の違いに応じて適切に変更することで、他の体液タイプに適用できます。結論として、この詳細で信頼性の高いプロトコルは、BEVの標準化された分離と精製を容易にし、その後のマルチオミクス分析と機能実験の基礎を築きます。

The gut is widely recognized as the organ harboring the most abundant microbial communities in the human body, with over 90% of bacteria involved in colonization and multiplication1,2. Extensive evidence has demonstrated that the gut microbiota modulates the gut microenvironment and simultaneously interacts with dysfunction in distant organs, primarily through an impaired intestinal barrier3,4. Mounting evidence indicates a correlation between the imbalance of gut microbiota and the progression of inflammatory bowel disease (IBD)5,6, as well as cognitive disorders through the gut-brain axis5,6,7,8. Bacterial extracellular vesicles (BEVs) produced by bacteria play significant roles in these pathological processes.
BEVs are nanoscale particles encapsulating bacterial derivatives, with diameters ranging from 20 to 400 nm. They have been demonstrated to facilitate interactions between bacteria and their host organisms9,10. Despite their invisibility, these particles have garnered increasing attention from researchers due to their prospective broad applications as diagnostic biomarkers, therapeutic targets, and drug delivery vehicles11. Human feces, often used as biospecimens for studying BEVs, predominantly sourced from gut bacteria, contain a complex mixture of water, bacteria, lipids, proteins, undigested food residue, and exfoliated epithelial cells among others. The intricate fecal composition poses challenges to the isolation and purity of BEVs, thereby impeding a comprehensive, objective, and realistic analysis of BEVs. Hence, effective strategies to minimize interference from contaminating components and enhance the yield of BEVs have emerged as critical issues warranting immediate attention.
Existing isolation strategies largely rely on techniques such as ultra-high-speed centrifugation (UC), density gradient centrifugation (DGC), and size exclusion chromatography (SEC)12,13,14,15,16,17. Currently, DGC is one of the most widely applied methods in the field of BEV separation, encompassing two sedimentation-floating modes, &#34;Top-down&#34; and &#34;Bottom-up&#34;, which are determined by the initial loading position of the sample. These methodologies differentiate extracellular vesicles (EVs) from other components based on size and density disparities, yielding variable purity and recovery rates. Prior research has indicated that single-approach strategies are insufficient for adequately separating EVs from soluble proteins in body fluid samples, such as lipoprotein in blood18 and Tamm-Horsfall protein in urine19. Additionally, the size distribution of eukaryotic extracellular vesicles (EEVs) often overlaps with that of BEVs, thereby necessitating further methodological enhancements to optimize BEV yield. Consequently, advancing the study of BEVs hinges on the development of effective separation and purification methodologies. Notably, Tulkens et al15 employed an orthogonal biophysical strategy to separate fecal BEVs from EEVs, in which the centrifugation time of a Bottom-up DGC mode was up to 18 h. In contrast, this study reduced it to 7 h, greatly saving the gradient-ultracentrifugation time and simplifying the process.
In the present study, we isolated and purified fecal BEVs employing two DGC modes under optimized buffer conditions, after enriching BEVs with a range of differential centrifugation speeds, from low to extremely high velocity. Evaluations based on morphology, particle size, and concentration indicated a commendable performance by this enhanced method. This study could serve as the foundation for future research, extending its applications to a broader domain, and offering insights into the heterogeneity of BEVs within the human body. It also contributes to the standardization of BEV separation and analysis techniques.

著者スポットライト:細菌の細胞外小胞の分離と不均一性に関する研究の加速 

密度勾配遠心分離法を用いたヒト糞便からの細菌細胞外小胞の単離と精製(英語)

Our study isolates, purifies, and characterize bacterial extracellular vesicles from physicists using density gradient centrifugation. We aim to address the separation of BEVs from contaminants and provide a reliable method for researchers. Our protocol reduces centrifugation time from 18 to 7 hours.Top down mode improves BEV separation and reduces contamination from liver proteins. Our method simplifies the separation of BEVs, setting a standard for future studies. It can be applied to other body fluids with appropriate modification, enhancing our understanding and facilitating the study of BEVs revealing their inherent heterogeneity within the human body.

BEV富化画分の分布の決定 細菌の細胞外小胞(BEV)濃縮画分の分布を決定するために、外径 340 nm での吸光度値を測定するためのブランクコントロールを確立し、測定値とヨウジキサノールガイドラインに基づいて各画分の密度を計算しました(ステップ 8.1)。 表2 は密度の結果を示しており、フラクションF4〜F9が細胞外小胞に典型的に関連する範囲内の密度を示したこ...

Watch this Scientific Journal Video about Accelerating Research on Bacterial Extracellular Vesicles Separation and Heterogeneity at JoVE.com

本研究では、密度勾配遠心分離(DGC) により ヒトの糞便から濃縮した細菌の細胞外小胞(BEV)を単離・精製する方法を説明し、形態、粒子径、濃度からBEVの物理的特性を特定し、臨床研究および科学研究におけるDGCアプローチの潜在的な応用について議論します。

Bacterial extracellular vesicles (BEVs) are nanovesicles derived from bacteria that play an active role in bacteria-bacteria and bacteria-host ...

私たちの研究では、密度勾配遠心分離を使用して、物理学者から細菌の細胞外小胞を分離、精製、および特性評価します。私たちは、BEVと汚染物質の分離に取り組み、研究者に信頼できる方法を提供することを目指しています。当社のプロトコルにより、遠心分離時間が18時間から7時間に短縮されます。トップダウンモードは、BEVの分離を改善し、肝臓タンパク質からの汚染を低減します。私たちの方法は、BEVの分離を簡素化し、将来の研究の基準を設定します。これは、適切な修正を行うことで他の体液にも適用でき、人体に固有の不均一性を明らかにするBEVの理解を深め、研究を促進します。

isolation-purification-bacterial-extracellular-vesicles-from-human

Research

JoVE Journal

Biology

Isolation and Purification of Bacterial Extracellular Vesicles from Human Feces Using Density Gradient Centrifugation

1.7K ビュー.  Southern Medical University. 私たちの研究では、密度勾配遠心分離を使用して、物理学者から細菌の細胞外小胞を分離、精製、および特性評価します。私たちは、BEVと汚染物質の分離に取り組み、研究者に信頼できる方法を提供することを目指しています。当社のプロトコルにより、遠心分離時間が18時間から7時間に短縮されます。トップダウンモードは、BEVの分離を改善し、肝臓タンパク質?...

ビデオ: 著者スポットライト:細菌の細胞外小胞の分離と不均一性に関する研究の加速 

Bacterial extracellular vesicles (BEVs) are nanovesicles derived from bacteria that play an active role in bacteria-bacteria and bacteria-host communication, transferring bioactive molecules such as proteins, lipids, and nucleic acids inherited from the parent bacteria. BEVs derived from the gut microbiota have effects within the gastrointestinal tract and can reach distant organs, resulting in significant implications for physiology and pathology. Theoretical investigations that explore the types, quantities, and roles of BEVs derived from human feces are crucial for understanding the secretion and function of BEVs from the gut microbiota. These investigations also necessitate an improvement in the current strategy for isolating and purifying BEVs.
This study optimized the isolation and purification process of BEVs by establishing two density gradient centrifugation (DGC) modes: Top-down and Bottom-up. The enriched distribution of BEVs was determined in fractions 6 to 8 (F6-F8). The effectiveness of the approach was evaluated based on particle morphology, size, concentration, and protein content. The particle and protein recovery rates were calculated, and the presence of specific markers was analyzed to compare the recovery and purity of the two DGC modes. The results indicated that the Top-down centrifugation mode had lower contamination levels and achieved a recovery rate and purity similar to that of the Bottom-up mode. A centrifugation time of 7 h was sufficient to achieve a fecal BEV concentration of 108/mg.
Apart from feces, this method could be applied to other body fluid types with proper modification according to the differences in components and viscosity. In conclusion, this detailed and reliable protocol would facilitate the standardized isolation and purification of BEVs and thus, lay a foundation for subsequent multi-omics analysis and functional experiments.

This study describes a method to isolate and purify bacterial extracellular vesicles (BEVs) enriched from human feces via density gradient centrifugation (DGC), identifies the physical characteristics of BEVs from morphology, particle size, and concentration, and discusses the potential applications of the DGC approach in clinical and scientific research.

生物学

Bacterial Extracellular Vesicles (BEVs) Enrichment from Human Faeces Using Differential Centrifugation Speeds

To begin, take the prepared human fecal samples. Cool the high speed refrigerated centrifuge to 4 degrees Celsius. Use PBS to adjust the weight of the sample tubes to 0.1 grams, and centrifuge them at 3, 000 G for 20 minutes at 4 degrees Celsius.Using a plastic pipette, transfer the supernatant into two 50 milliliter tubes, leaving 1 milliliter behind. Then, centrifuge the supernatant at 12, 000 G for 30 minutes at 4 degrees Celsius. Using a 20 milliliter syringe, aspirate the supernatant, and remove the needle from the syringe.Filter the liquid through 0.22 micrometer filters into 50 milliliter tubes. Next, wipe the bucket with 75%alcohol to eliminate any remaining contamination. Transfer approximately 30 milliliters of the filtered fecal supernatant into the ultracentrifuge tube.Fill the tube with approximately 8 milliliters of PBS, leaving a 3 millimeter gap from the tube's opening. Place the two ultracentrifuge tubes in opposing ultracentrifugation buckets, and equalize the weight of the two buckets using PBS. Load all buckets onto the rotor, irrespective of whether they are loaded with tubes.Place the samples in the centrifuge, initiate the vacuum and spin them at 160, 000 G for 70 minutes at 4 degrees Celsius. As soon as the centrifugation completes, release the chamber vacuum and open the door of the ultra centrifuge. Then, promptly remove the rotor.Transfer the buckets from the rotor to the rack, and pick up the tubes using a nipper. Discard the supernatant, and save the visible brown pellets. Add 1 milliliter of pre-chilled PBS to resuspend the pellets completely.Fill the tube with approximately 37 milliliters of PBS, leaving a 3 millimeter gap from the opening. After performing another round of ultracentrifugation, discard the supernatant and leave the tube inverted for 5 minutes. Remove any remaining solution on the inner wall with wipers.Using a 1, 000 microliter pipette, add 1.2 milliliters of pre-chilled PBS to resuspend pellets, and mix them by pipetting. Transfer 1.2 milliliters of the PBS BEV solution from one ultracentrifuge tube to a clean 1.5 milliliter micro tube.

遠心分離速度差を用いたヒト糞便からの細菌細胞外小胞(BEV)濃縮

Establishment of a Density Gradient Centrifugation System to Isolate and Purify Bacterial Extracellular Vesicles (BEVs) from Human Faeces

To begin, take 500 microliters of the prepared PBS/BEV solution. Combine it with three milliliters of PBS and mix gently using a 1, 000 microliter pipette. Place a 31 milliliter ultracentrifuge tube on a foam plate with holes, and label the tube with a downward arrow.Then hold a 1, 000 microliter pipette vertically and add three milliliters of the 50%iodixanol solution to the bottom of the tube. Place a tube holder slightly above the level of the foam plate below the tube opening, and tilt the tube to an angle of 70 degrees. Using a 1, 000 microliter pipette, add three milliliters of 40%iodixanol solution on top of the 50%iodixanol solution.Then layer three milliliters of 20%iodixanol solution on the 40%iodixanol solution. Using a 1, 000 microliter pipette, add three milliliters of a 10%iodixanol solution on top of the prepared 20%iodixanol solution. Next, add 3.5 milliliters of the PBS/BEV solution on top of the 10%iodixanol solution, and gently return the tubes to an upright position.Now, position a 31 milliliter ultracentrifuge tube on a foam plate with holes, and label it with an upward arrow. Using a 1, 000 microliter pipette, vertically add 2.5 milliliters of the 60%iodixanol stock solution into the bottom of the tube, and combine it with 500 microliters of PBS/BEV solution to get three milliliters of 50%iodixanol BEV solution. Mix the solution thoroughly by pipetting.Then after layering 40, 20 and 10%iodixanol solution in sequence, use a 1, 000 microliter pipette to add 3.5 milliliters of PBS on top of the 10%iodixanol solution. Adjust the weight of the two tubes with PBS to a total weight within plus minus 0.005 grams. Next, position the tubes in the buckets and centrifuge them at 160, 000 G for seven hours at four degrees Celsius.Using a pipetter, collect the fractions obtained from a gradient ultracentrifugation mode sequentially from top to bottom against the sidewall into 10 separate 38.5 milliliter ultracentrifuge tubes. Then ultracentrifuge the fractions at 160, 000 G for 70 minutes at four degrees Celsius. Remove the supernatant, and invert the ultracentrifuge tubes for five minutes.Next, resuspend the pellets in 200 microliters of pre-chilled PBS using a 200 microliter pipette. Transfer the PBS/BEV solution into a clean 1.5 milliliter microtube. Label the fractions from F1 to F10 as obtained from one gradient ultracentrifugation mode, and proceed for analysis.