AbstractSynthetic glycans (SGs) containing glycosidic linkages and structures not identified in nature offer a means for deliberately altering microbial community properties. Here pools of SG oligosaccharides were generated via polymerization of monosaccharides and screened for their ability to increase saccharolytic Bacteroides in ex vivo cultures of human fecal samples.

摘要含有糖苷键和自然界未鉴定结构的合成聚糖（SGs）为故意改变微生物群落特性提供了一种手段。。

A lead SG preparation was orally administered to gnotobiotic mice harboring a consortium of 56 cultured, phylogenetically diverse human gut bacteria and fed a Western diet. The abundances of 3 of 15 Bacteroides strains increased, most prominently B. intestinalis. Underlying mechanisms were characterized by analyzing in vivo expression of the carbohydrate utilization machinery, using retrievable microscopic paramagnetic particles with bound SG oligosaccharides and assaying SG degradation by individual purified B.

将铅SG制剂口服给含有56种培养的，系统发育多样的人类肠道细菌并喂食西方饮食的生殖生物小鼠。。通过分析碳水化合物利用机制的体内表达，使用具有结合的SG寡糖的可回收显微顺磁性颗粒并通过单个纯化的B测定SG降解来表征潜在的机制。

intestinalis glycoside hydrolases. The results reveal that SGs can selectively co-opt carbohydrate utilization machinery in different human gut Bacteroides and demonstrate a means for identifying artificial carbohydrate structures for targeted bacterial manipulation..

肠道糖苷水解酶。结果表明，SGs可以选择性地在不同的人类肠道类杆菌中选择碳水化合物利用机制，并证明了一种鉴定人工碳水化合物结构以进行靶向细菌操作的方法。。

MainIn nature, glycans are synthesized in a template-independent process that employs specific glycosyltransferases and activated monosaccharide donor sugars as substrates1,2. The structural diversity of naturally occurring glycans is limited by several mechanisms, including the pattern of expression of genes encoding glycosyltransferases, the linkage specificities of these enzymes, and the generation and availability of activated monosaccharide donors and suitable acceptors.

本质上，聚糖是在不依赖模板的过程中合成的，该过程使用特定的糖基转移酶和活化的单糖供体糖作为底物1,2。天然存在的聚糖的结构多样性受到几种机制的限制，包括编码糖基转移酶的基因的表达模式，这些酶的连锁特异性，以及活化的单糖供体和合适受体的产生和可用性。

Members of the phylum Bacteroidota are adept at metabolizing polysaccharides and have, through lateral gene transfer and/or genetic recombination, functionally diversified their genomes for utilization of various natural polysaccharides3. While estimates of natural glycan structural diversity are difficult to derive, estimates based on the number and diversity of degradative carbohydrate-active enzyme (CAZyme) gene clusters encoded in Bacteroidota genomes suggest that there are several thousand unique, naturally occurring structures4.

类杆菌门的成员擅长代谢多糖，并通过侧向基因转移和/或基因重组，使其基因组功能多样化，以利用各种天然多糖3。虽然很难得出天然聚糖结构多样性的估计值，但基于类杆菌基因组中编码的降解性碳水化合物活性酶（CAZyme）基因簇的数量和多样性的估计表明，存在数千种独特的天然结构4。

This value is multiple orders of magnitude less than what is theoretically possible5, emphasizing the constraints on biosynthetic processes that operate in and on living systems.Glycans that are generated synthetically can contain structures and linkage combinations not previously identified in nature.

这个值比理论上可能的值低几个数量级5，强调了对生命系统中和生命系统中的生物合成过程的限制。合成产生的聚糖可以含有先前在自然界中未鉴定的结构和连接组合。

A recently developed and generalizable approach for generating synthetic glycans (SGs) involves monosaccharide building blocks and a zwitterionic resin that catalyzes glycosidic bond formation between the reducing end of a monosaccharide and an acceptor hydroxyl on the growing SG6,7. By changing the monosaccharide starting material and reaction conditions, a pool of nonidentical, nonrepetitive oligosaccharides can be obtained in a fashion agnostic to biocatalysis or bio.

最近开发和推广的产生合成聚糖（SGs）的方法涉及单糖构建块和两性离子树脂，其催化单糖的还原端和生长的SG6,7上的受体羟基之间的糖苷键形成。通过改变单糖起始原料和反应条件，可以以与生物催化或生物不可知的方式获得不相同的非重复性寡糖库。

Data availability

数据可用性

Shotgun microbial community DNA sequencing and microbial RNA-seq datasets generated from gnotobiotic mice have been deposited at the European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena) under accession number PRJEB55381. MALDI-TOF MS data are available in GlycoPOST (https://glycopost.glycosmos.org/) under accession number GPST000301.

鸟枪微生物群落DNA测序和由gnotobiotic小鼠产生的微生物RNA-seq数据集已保存在欧洲核苷酸档案馆（ENA）；https://www.ebi.ac.uk/ena)登记号为PRJEB55381。MALDI-TOF MS数据可在GlycoPOST中获得(https://glycopost.glycosmos.org/)登录号为GPST000301。

Source data are provided with this paper..

本文提供了源数据。。

Code availability

代码可用性

Code for COPRO-Seq analysis is available at https://gitlab.com/Gordon_Lab/COPRO-Seq. Code for microbial RNA-seq analysis is available at https://gitlab.com/zbeller31/metatranscriptomics_pipeline.

https://gitlab.com/Gordon_Lab/COPRO-Seq.微生物RNA-seq分析代码可在https://gitlab.com/zbeller31/metatranscriptomics_pipeline.

ReferencesCaffall, K. H. & Mohnen, D. The structure, function, and biosynthesis of plant cell wall pectic polysaccharides. Carbohydr. Res. 344, 1879–1900 (2009).Article

参考文献Caffall，K.H。＆Mohnen，D。植物细胞壁果胶多糖的结构，功能和生物合成。碳水化合物。第3441879-1900号决议（2009年）。文章

PubMed

PubMed

CAS

中科院

Google Scholar

谷歌学者

Varki, A. Essentials of Glycobiology 3rd edn (Cold Spring Harbor Laboratory Press, 2017).Pudlo, N. A. et al. Phenotypic and genomic diversification in complex carbohydrate-degrading human gut bacteria. mSystems 7, e0094721 (2022).Article

Varki，A.《糖生物学基础》第三版（冷泉港实验室出版社，2017）。Pudlo，N.A.等人，《复杂碳水化合物降解人类肠道细菌的表型和基因组多样性》，mSystems 7，e0094721（2022）。文章

PubMed

PubMed

Google Scholar

谷歌学者

Lapébie, P., Lombard, V., Drula, E., Terrapon, N. & Henrissat, B. Bacteroidetes use thousands of enzyme combinations to break down glycans. Nat. Commun. 10, 2043 (2019).Article

Lapébie，P.，Lombard，V.，Drula，E.，Terrapon，N。＆Henrissat，B.Bacteroidetes使用数千种酶组合来分解聚糖。国家公社。102043（2019）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Laine, R. A. A calculation of all possible oligosaccharide isomers both branched and linear yields 1.05 × 1012 structures for a reducing hexasaccharide: the isomer barrier to development of single-method saccharide sequencing or synthesis systems. Glycobiology 4, 759–767 (1994).Article .

Laine，R.A。计算所有可能的支链和线性寡糖异构体，得到还原性六糖的1.05×1012个结构：异构体阻碍了单一方法糖测序或合成系统的发展。糖生物学4759-767（1994）。文章。

PubMed

PubMed

CAS

中科院

Google Scholar

谷歌学者

Geremia, J. M., Liu, C. M. & Murphy, A. V. Methods of producing glycan polymers. US Patent app 16/761115 (2020).Tolonen, A. C. et al. Synthetic glycans control gut microbiome structure and mitigate colitis in mice. Nat. Commun. 13, 1244 (2022).Article

Geremia，J.M.，Liu，C.M。和Murphy，A.V。生产聚糖聚合物的方法。美国专利申请16/761115（2020）。Tolonen，A.C。等人。合成聚糖控制肠道微生物组结构并减轻小鼠结肠炎。国家公社。131244（2022）。文章

PubMed

PubMed

PubMed Central

公共医学中心

CAS

中科院

Google Scholar

谷歌学者

Conner, A. H. & Anderson, L. The tautomerization and mutarotation of β-l-arabinopyranose. Participation of both furanose anomers. Carbohydr. Res. 25, 107–116 (1972).Article

Conner，A.H。＆Anderson，L。β-L-阿拉伯吡喃糖的互变异构和突变。两种呋喃糖异构体的参与。碳水化合物。第25107-116号决议（1972年）。文章

CAS

中科院

Google Scholar

谷歌学者

Desai, M. S. et al. A dietary fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility. Cell 167, 1339–1353 (2016).Article

Desai，M.S.等人。缺乏膳食纤维的肠道微生物群会降解结肠粘液屏障并增强病原体的易感性。细胞1671339-1353（2016）。文章

PubMed

PubMed

PubMed Central

公共医学中心

CAS

中科院

Google Scholar

谷歌学者

Ndeh, D. & Gilbert, H. J. Biochemistry of complex glycan depolymerisation by the human gut microbiota. FEMS Microbiol. Rev. 42, 146–164 (2018).Article

Ndeh，D。＆Gilbert，H.J。人类肠道微生物群复杂聚糖解聚的生物化学。FEMS微生物。修订版42146-164（2018）。文章

PubMed

PubMed

CAS

中科院

Google Scholar

谷歌学者

Van Treuren, W. & Dodd, D. Microbial contribution to the human metabolome: implications for health and disease. Annu. Rev. Pathol. 15, 345–369 (2020).Article

Van Treuren，W。＆Dodd，D。微生物对人类代谢组的贡献：对健康和疾病的影响。年。Pathol牧师。15345-369（2020）。文章

PubMed

PubMed

Google Scholar

谷歌学者

Porter, N. T. & Martens, E. C. The critical roles of polysaccharides in gut microbial ecology and physiology. Annu. Rev. Microbiol. 71, 349–369 (2017).Article

Porter，N.T。＆Martens，E.C。多糖在肠道微生物生态学和生理学中的关键作用。年。微生物修订版。71349-369（2017）。文章

PubMed

PubMed

CAS

中科院

Google Scholar

谷歌学者

Zhao, L. et al. Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes. Science 359, 1151–1156 (2018).Article

Zhao，L。等人。膳食纤维选择性促进肠道细菌缓解2型糖尿病。科学3591151-1156（2018）。文章

PubMed

PubMed

CAS

中科院

Google Scholar

谷歌学者

Millet, Y. A. et al. Modulation of the gut microbiome by novel synthetic glycans for the production of propionate and the reduction of cardiometabolic risk factors. Preprint at bioRxiv https://doi.org/10.1101/2022.04.04.487010 (2022).Kochetkov, N. K., Ott, A. Y. & Shashkov, A. S. Synthesis and 1H NMR and 13C spectroscopy of l-arabinopyranosyl biosides.

Millet，Y.A.等人。新型合成聚糖对肠道微生物组的调节，用于生产丙酸盐和减少心脏代谢危险因素。bioRxiv预印本https://doi.org/10.1101/2022.04.04.487010（2022年）。Kochetkov，N.K.，Ott，A.Y。＆Shashkov，A.S。l-阿拉伯吡喃糖苷的合成和1H NMR和13C光谱。

Russ. Chem. Bull. 35, 183–192 (1986).Article .

俄罗斯化学。公牛。35183-192（1986）。文章。

Google Scholar

谷歌学者

Wefers, D. & Bunzel, M. NMR spectroscopic profiling of arabinan and galactan structural elements. J. Agric. Food Chem. 64, 9559–9568 (2016).Article

Wefers，D。＆Bunzel，M。阿拉伯聚糖和半乳聚糖结构元素的NMR光谱分析。J、 农业。食品化学。649559-9568（2016）。文章

PubMed

PubMed

CAS

中科院

Google Scholar

谷歌学者

Westphal, Y. et al. Branched arabino-oligosaccharides isolated from sugar beet arabinan. Carbohydr. Res. 345, 1180–1189 (2010).Article

Westphal，Y。等人，从甜菜阿拉伯聚糖中分离出的分支阿拉伯寡糖。碳水化合物。第3451180-1189号决议（2010年）。文章

PubMed

PubMed

CAS

中科院

Google Scholar

谷歌学者

Hibberd, M. C. et al. The effects of micronutrient deficiencies on bacterial species from the human gut microbiota. Sci. Transl. Med. 9, eaal4069 (2017).Article

。科学。翻译。医学杂志9，eaal4069（2017）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Ridaura, V. K. et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 341, 1241214 (2013).Article

Ridaura，V.K。等人。双胞胎的肠道微生物群与肥胖不一致，可调节小鼠的代谢。科学3411241214（2013）。文章

PubMed

PubMed

Google Scholar

谷歌学者

McNulty, N. P. et al. The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. Sci. Transl. Med. 3, 106ra106 (2011).Article

McNulty，N.P.等人。发酵乳菌株联合体对生殖细胞小鼠和单卵双胞胎肠道微生物组的影响。科学。翻译。医学杂志3106RA106（2011）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Stämmler, F. et al. Adjusting microbiome profiles for differences in microbial load by spike-in bacteria. Microbiome 4, 28 (2016).Article

Stämmler，F.等人，《调整微生物组谱，以通过加入细菌来调整微生物负荷的差异》。微生物组4,28（2016）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Wolf, A. R. et al. Bioremediation of a common product of food processing by a human gut bacterium. Cell Host Microbe 26, 463–477 (2019).Article

Wolf，A.R.等人。人类肠道细菌对食品加工常见产物的生物修复。细胞宿主微生物26463-477（2019）。文章

PubMed

PubMed

PubMed Central

公共医学中心

CAS

中科院

Google Scholar

谷歌学者

Anderson, K. L. & Salyers, A. A. Biochemical evidence that starch breakdown by Bacteroides thetaiotaomicron involves outer membrane starch-binding sites and periplasmic starch-degrading enzymes. J. Bacteriol. 171, 3192–3198 (1989).Article

Anderson，K.L。＆Salyers，A.A。生化证据表明，拟杆菌（Bacteroides thetaiotaomicron）分解淀粉涉及外膜淀粉结合位点和周质淀粉降解酶。J、 细菌。1713192-3198（1989）。文章

PubMed

PubMed

PubMed Central

公共医学中心

CAS

中科院

Google Scholar

谷歌学者

Terrapon, N. et al. PULDB: the expanded database of polysaccharide utilization loci. Nucleic Acids Res. 46, D677–D683 (2018).Article

Terrapon，N。等人。PULDB：多糖利用基因座的扩展数据库。核酸研究46，D677–D683（2018）。文章

PubMed

PubMed

CAS

中科院

Google Scholar

谷歌学者

Martens, E. C. et al. Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts. PLoS Biol. 9, e1001221 (2011).Article

Martens，E.C.等人。两种人类肠道共生体对植物细胞壁多糖的识别和降解。《公共科学图书馆·生物学》。9，e1001221（2011）。文章

PubMed

PubMed

PubMed Central

公共医学中心

CAS

中科院

Google Scholar

谷歌学者

Patnode, M. L. et al. Interspecies competition impacts targeted manipulation of human gut bacteria by fiber-derived glycans. Cell 179, 59–73 (2019).Article

Patnode，M.L.等人。种间竞争影响纤维衍生聚糖对人类肠道细菌的靶向操作。细胞179,59-73（2019）。文章

PubMed

PubMed

PubMed Central

公共医学中心

CAS

中科院

Google Scholar

谷歌学者

Rogowski, A. et al. Glycan complexity dictates microbial resource allocation in the large intestine. Nat. Commun. 6, 7481 (2015).Article

Rogowski，A。等人。聚糖的复杂性决定了大肠中微生物资源的分配。国家公社。67481（2015）。文章

PubMed

PubMed

CAS

中科院

Google Scholar

谷歌学者

Beller, Z. W. et al. Inducible CRISPR-targeted ‘knockdown’ of human gut Bacteroides in gnotobiotic mice discloses glycan utilization strategies. Proc. Natl Acad. Sci. USA 120, e2311422120 (2023).Article

。程序。国家科学院。科学。美国120，e2311422120（2023）。文章

PubMed

PubMed

PubMed Central

公共医学中心

CAS

中科院

Google Scholar

谷歌学者

Aziz, R. K. et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9, 75 (2008).Article

Aziz，R.K.等人，《RAST服务器：使用子系统技术的快速注释》。BMC基因组学9,75（2008）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Davis, J. J. et al. The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. Nucleic Acids Res. 48, D606–D612 (2020).PubMed

Davis，J.J.等人，《PATRIC生物信息学资源中心：扩展数据和分析能力》。核酸研究48，D606–D612（2020）。PubMed出版社

CAS

中科院

Google Scholar

谷歌学者

Drula, E. et al. The carbohydrate-active enzyme database: functions and literature. Nucleic Acids Res. 50, D571–D577 (2022).Article

Drula，E。等人。碳水化合物活性酶数据库：功能和文献。核酸研究50，D571–D577（2022）。文章

PubMed

PubMed

CAS

中科院

Google Scholar

谷歌学者

Overbeek, R. et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 42, D206–D214 (2014).Article

。核酸研究42，D206–D214（2014）。文章

PubMed

PubMed

CAS

中科院

Google Scholar

谷歌学者

Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).Article

Love，M.I.，Huber，W。＆Anders，S。用DESeq2缓和了RNA-seq数据的倍数变化和分散估计。基因组生物学。15550（2014）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Korotkevich, G. et al. Fast gene set enrichment analysis. Preprint at bioRxiv https://doi.org/10.1101/060012 (2021).Egorova, K. S., Kondakova, A. N. & Toukach, P. V. Carbohydrate Structure Database: tools for statistical analysis of bacterial, plant and fungal glycomes. Database 2015, bav073 (2015).Article .

Korotkevich，G。等人。快速基因组富集分析。bioRxiv预印本https://doi.org/10.1101/060012（2021年）。Egorova，K.S.，Kondakova，A.N。和Toukach，P.V。碳水化合物结构数据库：细菌，植物和真菌糖组的统计分析工具。数据库2015，bav073（2015）。文章。

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Luis, A. S. et al. Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides. Nat. Microbiol. 3, 210–219 (2018).Article

Luis，A.S.等人。膳食果胶聚糖通过人类结肠类杆菌中的协调酶途径降解。自然微生物。3210-219（2018）。文章

PubMed

PubMed

CAS

中科院

Google Scholar

谷歌学者

Cartmell, A. et al. A surface endogalactanase in Bacteroides thetaiotaomicron confers keystone status for arabinogalactan degradation. Nat. Microbiol. 3, 1314–1326 (2018).Article

Cartmell，A。等人。拟杆菌（Bacteroides thetaiotaomicron）中的表面内切半乳聚糖酶赋予阿拉伯半乳聚糖降解的关键地位。自然微生物。31314-1326（2018）。文章

PubMed

PubMed

PubMed Central

公共医学中心

CAS

中科院

Google Scholar

谷歌学者

Fujita, K., Takashi, Y., Obuchi, E., Kitahara, K. & Suganuma, T. Characterization of a novel beta-l-arabinofuranosidase in Bifidobacterium longum: functional elucidation of a DUF1680 protein family member. J. Biol. Chem. 289, 5240–5249 (2014).Article

Fujita，K.，Takashi，Y.，Obuchi，E.，Kitahara，K。＆Suganuma，T。长双歧杆菌中新型β-l-阿拉伯呋喃糖苷酶的表征：DUF1680蛋白家族成员的功能阐明。J、 生物。化学。2895240–5249（2014）。文章

PubMed

PubMed

PubMed Central

公共医学中心

CAS

中科院

Google Scholar

谷歌学者

Kikuchi, A. et al. A novel glycoside hydrolase family 97 enzyme: bifunctional beta-l-arabinopyranosidase/alpha-galactosidase from Bacteroides thetaiotaomicron. Biochimie 142, 41–50 (2017).Article

Kikuchi，A。等人。一种新型糖苷水解酶家族97酶：来自拟杆菌（Bacteroides thetaiotaomicron）的双功能β-l-阿拉伯吡喃糖苷酶/α-半乳糖苷酶。生物化学142,41-50（2017）。文章

PubMed

PubMed

Google Scholar

谷歌学者

Almagro Armenteros, J. J. et al. Signal P 5.0 improves signal peptide predictions using deep neural networks. Nat. Biotechnol. 37, 420–423 (2019).Article

Almagro Armenteros，J.J.等人，《信号P 5.0》使用深度神经网络改进了信号肽预测。美国国家生物技术公司。37420-423（2019）。文章

PubMed

PubMed

CAS

中科院

Google Scholar

谷歌学者

Chang, C. et al. A novel transcriptional regulator of l-arabinose utilization in human gut bacteria. Nucleic Acids Res. 43, 10546–10559 (2015).PubMed

Chang，C.等人，《人类肠道细菌中l-阿拉伯糖利用的新型转录调节因子》，《核酸研究》4310546-10559（2015）。PubMed出版社

PubMed Central

公共医学中心

CAS

中科院

Google Scholar

谷歌学者

Bobik, T. A., Havemann, G. D., Busch, R. J., Williams, D. S. & Aldrich, H. C. The propanediol utilization (pdu) operon of Salmonella enterica serovar Typhimurium LT2 includes genes necessary for formation of polyhedral organelles involved in coenzyme B12-dependent 1,2-propanediol degradation.

Bobik，T.A.，Havemann，G.D.，Busch，R.J.，Williams，D.S。＆Aldrich，H.C。肠道沙门氏菌血清型鼠伤寒沙门氏菌LT2的丙二醇利用（pdu）操纵子包括形成参与辅酶B12依赖性1,2-丙二醇降解的多面体细胞器所必需的基因。

J. Bacteriol. 181, 5967–5975 (1999).Article .

J.细菌醇。181, 5967-5975 (1999).第[UNK]条。

PubMed

PubMed

PubMed Central

公共医学中心

CAS

中科院

Google Scholar

谷歌学者

Wesener, D. A. et al. Microbiota functional activity biosensors for characterizing nutrient metabolism in vivo. Elife 10, e64478 (2021).Article

Wesener，D.A。等人。用于表征体内营养代谢的微生物群功能活性生物传感器。Elife 10，e64478（2021）。文章

PubMed

PubMed

PubMed Central

公共医学中心

CAS

中科院

Google Scholar

谷歌学者

Lees, A., Nelson, B. L. & Mond, J. J. Activation of soluble polysaccharides with 1-cyano-4-dimethylaminopyridinium tetrafluoroborate for use in protein–polysaccharide conjugate vaccines and immunological reagents. Vaccine 14, 190–198 (1996).Article

Lees，A.，Nelson，B.L。＆Mond，J.J。用1-氰基-4-二甲氨基吡啶四氟硼酸盐活化可溶性多糖，用于蛋白质-多糖缀合物疫苗和免疫试剂。疫苗14190-198（1996）。文章

PubMed

PubMed

CAS

中科院

Google Scholar

谷歌学者

Arnal, G., Attia, M. A., Asohan, J. & Brumer, H. A low-volume, parallel copper-bicinchoninic acid (BCA) assay for glycoside hydrolases. Methods Mol. Biol. 1588, 3–14 (2017).Article

Arnal，G.，Attia，M.A.，Asohan，J。＆Brumer，H。用于糖苷水解酶的低体积平行铜二辛可宁酸（BCA）测定。方法分子生物学。1588,3-14（2017）。文章

PubMed

PubMed

CAS

中科院

Google Scholar

谷歌学者

McNulty, N. P. et al. Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome. PLoS Biol. 11, e1001637 (2013).Article

McNulty，N.P.等人。饮食对含有纤维素拟杆菌WH2的模型人类肠道微生物群资源利用的影响，纤维素拟杆菌WH2是一种具有广泛糖生物群的共生体。《公共科学图书馆·生物学》。11，e1001637（2013）。文章

PubMed

PubMed

PubMed Central

公共医学中心

CAS

中科院

Google Scholar

谷歌学者

Al-Jourani, O. et al. Identification of d-arabinan-degrading enzymes in mycobacteria. Nat. Commun. 14, 2233 (2023).Article

。142233（2023）。文章

PubMed

PubMed

PubMed Central

公共医学中心

CAS

中科院

Google Scholar

谷歌学者

Feng, J. et al. Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions. Cell Host Microbe 30, 200–215 (2022).Article

Feng，J.等人。拟杆菌中的多糖利用位点决定了种群适应性和社区水平的相互作用。细胞宿主微生物30200–215（2022）。文章

PubMed

PubMed

PubMed Central

公共医学中心

CAS

中科院

Google Scholar

谷歌学者

Scott, M., Gunderson, C. W., Mateescu, E. M., Zhang, Z. & Hwa, T. Interdependence of cell growth and gene expression: origins and consequences. Science 330, 1099–1102 (2010).Article

Scott，M.，Gunderson，C.W.，Mateescu，E.M.，Zhang，Z.＆Hwa，T。细胞生长和基因表达的相互依赖性：起源和后果。科学3301099-1102（2010）。文章

PubMed

PubMed

CAS

中科院

Google Scholar

谷歌学者

Nasseri, S. A. et al. An alternative broad-specificity pathway for glycan breakdown in bacteria. Nature 631, 199–206 (2024).Article

Nasseri，S.A.等人，《细菌中聚糖分解的另一种广泛特异性途径》，《自然》631199-206（2024）。文章

PubMed

PubMed

CAS

中科院

Google Scholar

谷歌学者

Heux, S., Philippe, B. & Portais, J. C. High-throughput workflow for monitoring and mining bioprocess data and its application to inferring the physiological response of Escherichia coli to perturbations. Appl. Environ. Microbiol. 77, 7040–7049 (2011).Article

Heux，S.，Philippe，B。＆Portais，J.C。用于监测和挖掘生物过程数据的高通量工作流程及其在推断大肠杆菌对扰动的生理反应中的应用。应用。环境。微生物。。文章

PubMed

PubMed

PubMed Central

公共医学中心

CAS

中科院

Google Scholar

谷歌学者

Caporaso, J. G. et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl Acad. Sci. USA 108, 4516–4522 (2011).Article

Caporaso，J.G.等人。每个样本深度为数百万个序列的16S rRNA多样性的全球模式。程序。国家科学院。科学。美国1084516-4522（2011）。文章

PubMed

PubMed

CAS

中科院

Google Scholar

谷歌学者

Edgar, R. C. UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing. Preprint at bioRxiv https://doi.org/10.1101/081257 (2016).Callahan, B. J. et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).Article .

Edgar，R。C。UNOISE2：改进了Illumina 16S及其扩增子测序的错误校正。bioRxiv预印本https://doi.org/10.1101/081257（2016年）。Callahan，B。J。等人。DADA2：从Illumina扩增子数据推断高分辨率样品。自然方法13581-583（2016）。文章。

PubMed

PubMed

PubMed Central

公共医学中心

CAS

中科院

Google Scholar

谷歌学者

Turner, S., Pryer, K. M., Miao, V. P. & Palmer, J. D. Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis. J. Eukaryot. Microbiol. 46, 327–338 (1999).Article

Turner，S.，Pryer，K.M.，Miao，V.P。和Palmer，J.D。通过小亚基rRNA序列分析研究蓝藻和质体之间的深层系统发育关系。J、 真核生物。微生物。46327-338（1999）。文章

PubMed

PubMed

CAS

中科院

Google Scholar

谷歌学者

Goodman, A. L. et al. Identifying genetic determinants needed to establish a human gut symbiont in its habitat. Cell Host Microbe 6, 279–289 (2009).Article

Goodman，A.L.等人，确定在其栖息地建立人类肠道共生体所需的遗传决定因素。细胞宿主微生物6279-289（2009）。文章

PubMed

PubMed

PubMed Central

公共医学中心

CAS

中科院

Google Scholar

谷歌学者

Adey, A. et al. Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biol. 11, R119 (2010).Article

Adey，A。等人。通过高密度体外转座快速，低输入，低偏差构建鸟枪片段文库。基因组生物学。11，R119（2010）。文章

PubMed

PubMed

PubMed Central

公共医学中心

CAS

中科院

Google Scholar

谷歌学者

Boutet, E. et al. UniProtKB/Swiss-Prot, the manually annotated section of the UniProt KnowledgeBase: how to use the entry view. Methods Mol. Biol. 1374, 23–54 (2016).Article

Boutet，E.等人。UniProtKB/Swiss-Prot，UniProt知识库的手动注释部分：如何使用条目视图。方法分子生物学。1374,23-54（2016）。文章

PubMed

PubMed

CAS

中科院

Google Scholar

谷歌学者

Price, M. N. & Arkin, A. P. PaperBLAST: text mining papers for information about homologs. mSystems 2, e00039 (2017).Article

Price，M.N。和Arkin，A.P。PaperBLAST：有关同源物信息的文本挖掘论文。mSystems 2，e00039（2017）。文章

PubMed

PubMed

PubMed Central

公共医学中心

CAS

中科院

Google Scholar

谷歌学者

Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 17, 10–12 (2011).Article

Martin，M。Cutadapt从高通量测序读数中删除了衔接子序列。EMBnet。J、 。文章

Google Scholar

谷歌学者

Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).Article

Dobin，A。等人STAR：超快通用RNA-seq比对仪。生物信息学29,15-21（2013）。文章

PubMed

PubMed

CAS

中科院

Google Scholar

谷歌学者

Andrews, S. FastQC: a quality control tool for high throughput sequence data. Babraham Bioinformatics http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (2010).Guy, L., Kultima, J. R. & Andersson, S. G. genoPlotR: comparative gene and genome visualization in R. Bioinformatics 26, 2334–2335 (2010).Article .

Andrews，S。FastQC：高通量序列数据的质量控制工具。巴巴拉姆生物信息学http://www.bioinformatics.babraham.ac.uk/projects/fastqc/（2010年）。Guy，L.，Kultima，J.R。＆Andersson，S.G。genoPlotR:R.Bioinformatics 262334-2335（2010）中的比较基因和基因组可视化。文章。

PubMed

PubMed

PubMed Central

公共医学中心

CAS

中科院

Google Scholar

谷歌学者

Soto-Cantu, E., Cueto, R., Koch, J. & Russo, P. S. Synthesis and rapid characterization of amine-functionalized silica. Langmuir 28, 5562–5569 (2012).Article

Soto Cantu，E.，Cueto，R.，Koch，J。＆Russo，P.S。胺官能化二氧化硅的合成和快速表征。朗缪尔285562-5569（2012）。文章

PubMed

PubMed

CAS

中科院

Google Scholar

谷歌学者

Wehrens, R., Weingart, G. & Mattivi, F. metaMS: an open-source pipeline for GC-MS-based untargeted metabolomics. J. Chromatogr. B 966, 109–116 (2014).Article

Wehrens，R.，Weingart，G。＆Mattivi，F。metaMS：基于GC-MS的非靶向代谢组学的开源管道。J、 色谱仪。B 966109-116（2014）。文章

CAS

中科院

Google Scholar

谷歌学者

Heiss, C., Klutts, J. S., Wang, Z., Doering, T. L. & Azadi, P. The structure of Cryptococcus neoformans galactoxylomannan contains beta-d-glucuronic acid. Carbohydr. Res. 344, 915–920 (2009).Article

Heiss，C.，Klutts，J.S.，Wang，Z.，Doering，T.L。＆Azadi，P。新型隐球菌半乳糖基甘露聚糖的结构含有β-d-葡萄糖醛酸。碳水化合物。第344915–920号决议（2009年）。文章

PubMed

PubMed

PubMed Central

公共医学中心

CAS

中科院

Google Scholar

谷歌学者

Gibb, S. & Strimmer, K. MALDIquant: a versatile R package for the analysis of mass spectrometry data. Bioinformatics 28, 2270–2271 (2012).Article

Gibb，S。＆Strimmer，K。MALDIquant：用于分析质谱数据的多功能R软件包。生物信息学282270-2271（2012）。文章

PubMed

PubMed

CAS

中科院

Google Scholar

谷歌学者

Download referencesAcknowledgementsWe thank D. O’Donnell, M. Karlsson and J. Serugo for their invaluable assistance with mouse husbandry, M. Meier for generating shotgun sequencing and microbial RNA-seq datasets, A. Krezel for processing two-dimensional nuclear magnetic resonance spectra, S.

下载参考文献致谢我们感谢D.O'Donnell，M.Karlsson和J.Serugo在小鼠饲养方面的宝贵帮助，M.Meier生成鸟枪测序和微生物RNA-seq数据集，A.Krezel处理二维核磁共振光谱，S。

Henrissat for CAZyme predictions, J. Cheng for SCFA analysis, and K. Woolum and I. Artsimovitch for their assistance in expressing and purifying GH enzymes. This work was supported by grants from the NIH (DK30292 and DK70977 to J.I.G.) and an academic industrial collaboration between Washington University and Kaleido Biosciences.

Henrissat进行CAZyme预测，J.Cheng进行SCFA分析，K.Woolum和I.Artsimovitch协助表达和纯化GH酶。这项工作得到了美国国立卫生研究院的资助（DK30292和DK70977授予J.I.G.）以及华盛顿大学和卡莱多生物科学之间的学术工业合作的支持。

D.A.W. is the recipient of a career development award from the NIH (AT011374) and was a Damon Runyon Fellow supported by the Damon Runyon Cancer Research Foundation (DRG–2303–17). Z.W.B. is the recipient of a predoctoral MD/PhD career development fellowship from the NIH (F30 DK123838) and is a member of the Washington University Medical Scientist Training Program (supported by NIH grant GM007200).

D、 A.W.是美国国立卫生研究院职业发展奖（AT011374）的获得者，也是Damon Runyon癌症研究基金会（DRG-2303-17）支持的Damon Runyon研究员。Z、 W.B.是美国国立卫生研究院博士前医学博士/博士职业发展奖学金（F30 DK123838）的获得者，也是华盛顿大学医学科学家培训计划（由美国国立卫生研究院拨款GM007200支持）的成员。

The Biomedical Mass Spectrometry Resource at Washington University is supported by NIH grants R24GM136766, P30DK020579 and R21AI144658.Author informationAuthors and AffiliationsEdison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USADarryl A.

华盛顿大学的生物医学质谱资源得到了美国国立卫生研究院拨款R24GM136766，P30DK020579和R21AI144658的支持。作者信息作者和附属机构华盛顿大学医学院基因组科学和系统生物学家庭中心，美国密苏里州圣路易斯。

Wesener, Zachary W. Beller & Jeffrey I. GordonCenter for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USADarryl A. Wesener, Zachary W. Beller & Jeffrey I. GordonDepartment of Microbiology, The Ohio State University, Columbus, OH, USADarryl A. Wesener & Megan F.

Wesener，Zachary W.Beller＆Jeffrey I.Gordon华盛顿大学医学院肠道微生物组与营养研究中心，密苏里州圣路易斯，USADarryl A.Wesener，Zachary W.Beller＆Jeffrey I.Gordon俄亥俄州立大学微生物学系，俄亥俄州哥伦布，USADarryl A.Wesener＆Megan F。

HillKaleido Biosciences, Lexington, MA, USAHan Yuan, David B. Belanger & Johan E. T. van Hylckama VliegBiomedical Mass Spectrometry Reso.

HillKaleido Biosciences，马萨诸塞州列克星敦，USAHan Yuan，David B.Belanger＆Johan E.T.van Hylckama VliegBiomedical Mass Spectrometry Reso。

PubMed Google ScholarZachary W. BellerView author publicationsYou can also search for this author in

PubMed Google ScholarMegan F. HillView author publicationsYou can also search for this author in

PubMed Google Scholarmamegan F.HillView作者出版物您也可以在

PubMed Google ScholarHan YuanView author publicationsYou can also search for this author in

PubMed Google ScholarHan YuanView作者出版物您也可以在

PubMed Google ScholarDavid B. BelangerView author publicationsYou can also search for this author in

PubMed Google ScholarDavid B.BelangerView作者出版物您也可以在

PubMed Google ScholarCheryl FrankfaterView author publicationsYou can also search for this author in

PubMed Google Scholarreyl FrankfaterView作者出版物您也可以在

PubMed Google ScholarNicolas TerraponView author publicationsYou can also search for this author in

PubMed Google ScholarNicolas TerraponView作者出版物您也可以在

PubMed Google ScholarBernard HenrissatView author publicationsYou can also search for this author in

PubMed Google ScholarBernard HenrissatView作者出版物您也可以在

PubMed Google ScholarDmitry A. RodionovView author publicationsYou can also search for this author in

PubMed Google ScholarDmitry A.RodionovView作者出版物您也可以在

PubMed Google ScholarSemen A. LeynView author publicationsYou can also search for this author in

PubMed Google ScholarSemen A.LeynView作者出版物您也可以在

PubMed Google ScholarAndrei OstermanView author publicationsYou can also search for this author in

PubMed Google ScholarAndrei OstermanView作者出版物您也可以在

PubMed Google ScholarJohan E. T. van Hylckama VliegView author publicationsYou can also search for this author in

PubMed Google ScholarJohan E.T.van Hylckama VliegView作者出版物您也可以在

PubMed Google ScholarJeffrey I. GordonView author publicationsYou can also search for this author in

PubMed谷歌学者Jeffrey I.GordonView作者出版物您也可以在

PubMed Google ScholarContributionsD.A.W. and J.I.G. designed the gnotobiotic mouse experiments, which were performed by D.A.W. Shotgun sequencing and microbial RNA-seq datasets were generated by D.A.W. and analyzed by D.A.W., Z.W.B., N.T., B.H., D.A.R., S.A.L. and A.O. D.B.B., H.Y.

PubMed谷歌学术贡献SD。A、 W.和J.I.G.设计了gnotobiotic小鼠实验，该实验由D.A.W.鸟枪测序进行，微生物RNA-seq数据集由D.A.W.生成，并由D.A.W.，Z.W.B.，N.T.，B.H.，D.A.R.，S.A.L.和A.O.D.B.B.，H.Y.进行分析。

and J.E.T.v.H.V selected candidate SGs and collected data on their chemical properties and biological activities. D.A.W., H.Y. and C.F. developed carbohydrate analytical procedures and performed the analyses. H.Y. collected glycosyl linkage data. C.F. collected MALDI-TOF MS data. M.F.H. expressed, purified and quantified GH activities.

和J.E.T.v.H.v选择了候选SG，并收集了其化学性质和生物活性的数据。D、 A.W.，H.Y.和C.F.开发了碳水化合物分析程序并进行了分析。H、 Y.收集糖基连接数据。C、 F.收集MALDI-TOF MS数据。M、 F.H.表达，纯化和定量GH活性。

D.A.W. synthesized and analyzed MFABs. D.A.W. and J.I.G. wrote this paper with invaluable assistance from co-authors.Corresponding authorsCorrespondence to.

D、 A.W.合成并分析了MFAB。D、 A.W.和J.I.G.在合著者的宝贵帮助下撰写了这篇论文。通讯作者通讯。

Darryl A. Wesener or Jeffrey I. Gordon.Ethics declarations

Darryl A.Wesener或Jeffrey I.Gordon。道德宣言

Competing interests

相互竞争的利益

A.O. and D.A.R. are co-founders of Phenobiome Inc., a company pursuing development of computational tools for predictive phenotype profiling of microbial communities. H.Y., D.B.B. and J.E.T.v.H.V. were employees of Kaleido Biosciences, a company that sought to commercialize SGs as agents to manipulate human gut bacteria.

A、 O.和D.A.R.是Phenobiome Inc.的联合创始人，该公司致力于开发用于预测微生物群落表型分析的计算工具。H、 Y.，D.B.B.和J.E.T.v.H.v.是Kaleido Biosciences的员工，该公司试图将SGs商业化为操纵人类肠道细菌的试剂。

H.Y. is an inventor on a patent related to the production and use of SGs (US20200390798A1). D.A.W. and J.I.G. are listed as inventors on a patent application related to using particles to measure microbiota enzymatic activities (WO2021016133A1). The other authors declare no competing interests..

H、 Y.是SGs（US20200390798A1）生产和使用相关专利的发明人。D、 A.W.和J.I.G.被列为与使用颗粒测量微生物群酶活性有关的专利申请的发明人（WO2021016133A1）。其他作者声明没有利益冲突。。

Peer review

同行评审

Peer review information

同行评审信息

Nature Chemical Biology thanks Sabina La Rosa and the other, anonymous, reviewers for their contribution to the peer review of this work.

《自然化学生物学》感谢Sabina La Rosa和其他匿名审稿人为这项工作的同行评审做出的贡献。

Additional informationPublisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.Extended dataExtended Data Fig. 1 Structural analysis of SG10.a, Log2 fold-change in the fractional abundance of bacterial taxa (genus level) in ex vivo cultures of human fecal samples in medium supplemented with the indicated SG preparations.

Additional informationPublisher的注释Springer Nature在已发布的地图和机构隶属关系中的管辖权主张方面保持中立。扩展数据扩展数据图1 SG10的结构分析。在补充有所示SG制剂的培养基中，人粪便样品的离体培养物中细菌类群（属水平）的分数丰度的Log2倍变化。

Each point represents the mean of triplicate fermentations from one of five human donor communities; the shape of each point signifies the fecal community. The central bar in the box plot represents the median, the hinges represent the first and third quartiles, and the box plot whiskers represent data points within 1.5 times the interquartile range.

每个点代表来自五个人类供体社区之一的一式三份发酵的平均值；每个点的形状表示粪便群落。箱形图中的中心条表示中位数，铰链表示第一和第三四分位数，箱形图晶须表示四分位间距1.5倍内的数据点。

b, Glycosyl linkage analysis of SG10. Each data point represents an independent sample preparation (n = 3). Bars represent the mean. Error bars represent the s.d. c, Anomeric region of a 2D (1H,13C)-HSQC NMR spectra of SG10. Linkages joined by beta anomeric bonds are expected to have 13C chemical shifts (F1 axis) of 97–102 ppm based on previous literature15,16,17.Source dataExtended Data Fig.

b、 SG10的糖基连接分析。每个数据点代表一个独立的样品制备（n=3）。条形代表平均值。误差线表示SG10的2D（1H，13C）-HSQC NMR光谱的s.d.c，异头区域。。

2 Absolute abundances of selected bacteria in gnotobiotic mice.a, Data from cecal contents. Each data point represents a single mouse (n = 8). Bars represents the mean. Error bars represent the s.d. Color denotes treatment group. P values were calculated using a one-way ANOVA and are FDR-corrected. b, Fecal data.

2无菌小鼠中所选细菌的绝对丰度。a，盲肠内容物的数据。每个数据点代表一只鼠标（n=8）。条形代表平均值。误差线表示s.d。颜色表示治疗组。使用单因素方差分析计算P值，并进行FDR校正。b、 粪便数据。

Each point represents a single mouse (n = 8). Bars represents the mean. Error bars represent the s.d. Shaded regions highlight timepoints during SG10 supplementation. P values were calculated using a linear mixed-effects model (Gaussian) and are FDR-corrected.Extended Data Fig. 3 Quantification of short-chain fatty acids in mouse cec.

每个点代表一只鼠标（n=8）。条形代表平均值。误差线表示s.d.阴影区域突出显示补充SG10期间的时间点。。扩展数据图3小鼠cec中短链脂肪酸的定量。

Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material.

开放获取本文是根据知识共享署名非商业性NoDerivatives 4.0国际许可证授权的，该许可证允许以任何媒介或格式进行任何非商业性使用，共享，分发和复制，只要您对原始作者和来源给予适当的信任，提供知识共享许可证的链接，并指出您是否修改了许可材料。

You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.

根据本许可证，您无权共享源自本文或其部分的改编材料。本文中的图像或其他第三方材料包含在文章的知识共享许可证中，除非该材料的信用额度中另有说明。如果材料未包含在文章的知识共享许可中，并且您的预期用途不受法律法规的许可或超出许可用途，则您需要直接获得版权所有者的许可。

To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/..

要查看此许可证的副本，请访问http://creativecommons.org/licenses/by-nc-nd/4.0/..

Reprints and permissionsAbout this articleCite this articleWesener, D.A., Beller, Z.W., Hill, M.F. et al. In vivo manipulation of human gut Bacteroides fitness by abiotic oligosaccharides.

转载和许可本文引用本文Wesener，D.A.，Beller，Z.W.，Hill，M.F.等人通过非生物寡糖体内操纵人类肠道拟杆菌的适应性。

Nat Chem Biol (2024). https://doi.org/10.1038/s41589-024-01763-6Download citationReceived: 03 May 2023Accepted: 27 September 2024Published: 23 October 2024DOI: https://doi.org/10.1038/s41589-024-01763-6Share this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy to clipboard.

Nat Chem Biol（2024）。https://doi.org/10.1038/s41589-024-01763-6Download引文接收日期：2023年5月3日接收日期：2024年9月27日发布日期：2024年10月23日OI：https://doi.org/10.1038/s41589-024-01763-6Share本文与您共享以下链接的任何人都可以阅读此内容：获取可共享链接对不起，本文目前没有可共享的链接。复制到剪贴板。

Provided by the Springer Nature SharedIt content-sharing initiative

由Springer Nature SharedIt内容共享计划提供