畜牧兽医学报 ›› 2021, Vol. 52 ›› Issue (5): 1186-1194.doi: 10.11843/j.issn.0366-6964.2021.05.005
周梦情, 陈从英*
收稿日期:
2020-10-22
出版日期:
2021-05-23
发布日期:
2021-05-22
通讯作者:
陈从英,主要从事肠道菌群与宿主基因互作研究,E-mail:Chcy75@hotmail.com
作者简介:
周梦情(1996-),女,江西上饶人,硕士生,主要从事猪肠道菌群与宿主基因互作研究,E-mail:1473713356@qq.com
基金资助:
ZHOU Mengqing, CHEN Congying*
Received:
2020-10-22
Online:
2021-05-23
Published:
2021-05-22
摘要: 猪肠道菌群是由所有定殖在猪肠道里的大量细菌、病毒、真菌和古菌等构成的集合。已有研究表明,很多疾病以及猪重要经济性状都与肠道菌群有关。目前,肠道菌群研究使用较多的技术是16S rRNA基因测序和宏基因组测序,但这些技术并不能了解具体菌株的实际功能和生理特性。肠道细菌的分离培养具有特殊重要的意义。近几年来,肠道细菌的培养取得了重要进展,基于培养条件的多样性分离培养出了更多的肠道细菌类别,这对促进肠道菌群在菌株水平的研究以及推广应用有重要意义。本文主要从猪肠道菌群组成结构、培养组学发展、猪肠道细菌培养组学的研究现状等方面进行论述和展望,为后续猪肠道菌群菌株的功能和影响表型的机制研究提供参考借鉴。
中图分类号:
周梦情, 陈从英. 猪肠道细菌培养组学研究进展[J]. 畜牧兽医学报, 2021, 52(5): 1186-1194.
ZHOU Mengqing, CHEN Congying. Research Progress on Intestinal Bacteria Culturomics of Pigs[J]. Acta Veterinaria et Zootechnica Sinica, 2021, 52(5): 1186-1194.
[1] | XIAO L,ESTELLÉ J,KIILERICH P,et al.A reference gene catalogue of the pig gut microbiome[J].Nat Microbiol,2016, 1(12):16161. |
[2] | JANDA J M,ABBOTT S L.16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory:pluses,perils,and pitfalls[J]. J Clin Microbiol,2007,45(9):2761-2764. |
[3] | TRUONG D T,TETT A,PASOLLI E,et al.Microbial strain-level population structure and genetic diversity from metagenomes[J]. Genome Res,2017,27(4):626-638. |
[4] | WALKER A W,DUNCAN S H,LOUIS P,et al.Phylogeny,culturing,and metagenomics of the human gut microbiota[J].Trends Microbiol,2014,22(5):267-274. |
[5] | HU J,MA L B,NIE Y F,et al.A microbiota-derived bacteriocin targets the host to confer diarrhea resistance in early-weaned piglets[J].Cell Host Microbe,2018,24(6):817-832.e8. |
[6] | 宋连喜,鄂禄祥,高明,等.猪和兔胚胎胃肠道菌群的初步研究[J].中国兽医杂志,2007,43(10):24-26.SONG L X,E L X,GAO M,et al.Preliminary study of the flora in the gastrointestinal tract of embryos of pigs and rabbits[J].Chinese Journal of Veterinary Medicine,2007,43(10):24-26.(in Chinese) |
[7] | MOELLER A H,SUZUKI T A,PHIFER-RIXEY M,et al.Transmission modes of the mammalian gut microbiota[J].Science, 2018,362(6413):453-457. |
[8] | WANG X F,TSAI T,DENG F L,et al.Longitudinal investigation of the swine gut microbiome from birth to market reveals stage and growth performance associated bacteria[J].Microbiome,2019,7(1):109. |
[9] | XU F Z,FU Y Q,SUN T Y,et al.The interplay between host genetics and the gut microbiome reveals common and distinct microbiome features for complex human diseases[J].Microbiome,2020,8(1):145. |
[10] | HE M Z,GAO J,WU J Y,et al.Host gender and androgen levels regulate gut bacterial taxa in pigs leading to sex-biased serum metabolite profiles[J].Front Microbiol,2019,10:1359. |
[11] | MACKIE R I,SGHIR A,GASKINS H R.Developmental microbial ecology of the neonatal gastrointestinal tract[J].Am J Clin Nutr,1999,69(5):1035s-1045s. |
[12] | QIN J J,LI R Q,RAES J,et al.A human gut microbial gene catalogue established by metagenomic sequencing[J]. Nature, 2010, 464(7285):59-65. |
[13] | SCHWALM III N D,GROISMAN E A.Navigating the gut buffet:control of polysaccharide utilization in Bacteroides spp.[J].Trends Microbiol,2017,25(12):1005-1015. |
[14] | KUGADAS A,WRIGHT Q,GEDDES-MCALISTER J,et al.Role of microbiota in strengthening ocular mucosal barrier function through secretory IgA[J].Invest Ophthalmol Vis Sci,2017,58(11):4593-4600. |
[15] | NATIVIDAD J M,AGUS A,PLANCHAIS J,et al.Impaired aryl hydrocarbon receptor ligand production by the gut microbiota is a key factor in metabolic syndrome[J].Cell Metab,2018,28(5):737-749. |
[16] | LEVY M,BLACHER E,ELINAV E.Microbiome,metabolites and host immunity[J].Curr Opin Microbiol,2017,35:8-15. |
[17] | GUO H,CHOU W C,LAI Y J,et al.Multi-omics analyses of radiation survivors identify radioprotective microbes and metabolites[J].Science,2020,370(6516):eaay9097. |
[18] | KRAUTKRAMER K A,FAN J,BÄCKHED F.Gut microbial metabolites as multi-kingdom intermediates[J].Nat Rev Microbiol, 2021,19(2):77-94. |
[19] | VISCONTI A,LE ROY C I,ROSA F,et al.Interplay between the human gut microbiome and host metabolism[J].Nat Commun,2019, 10(1):4505. |
[20] | SANNA S,VAN ZUYDAM N R,MAHAJAN A,et al.Causal relationships among the gut microbiome,short-chain fatty acids and metabolic diseases[J].Nat Genet,2019,51(4):600-605. |
[21] | 张柏林,秦贵信,孙泽威,等.仔猪胃肠道微生物菌群定植规律及其功能的研究进展[J].中国畜牧杂志,2009,45(19):66-69.ZHANG B L,QIN G X,SUN Z W,et al.Advances in gastrointestinal microflora colonization rule and function of piglet[J].Chinese Journal of Animal Science,2009,45(19):66-69.(in Chinese) |
[22] | KIM H B,BOREWICZ K,WHITE B A,et al.Longitudinal investigation of the age-related bacterial diversity in the feces of commercial pigs[J].Vet Microbiol,2011,153(1-2):124-133. |
[23] | PATIL Y,GOONERATNE R,JU X H.Interactions between host and gut microbiota in domestic pigs:a review[J].Gut Microbes,2020,11(3):310-334. |
[24] | HAN G G,LEE J,JIN G,et al.Tracing of the fecal microbiota of commercial pigs at five growth stages from birth to shipment[J].Sci Rep,2018,8(1):6012. |
[25] | RAMAYO-CALDAS Y,MACH N,LEPAGE P,et al.Phylogenetic network analysis applied to pig gut microbiota identifies an ecosystem structure linked with growth traits[J].ISME J,2016,10(12):2973-2977. |
[26] | LAGIER J C,ARMOUGOM F,MILLION M,et al.Microbial culturomics:paradigm shift in the human gut microbiome study[J].Clin Microbiol Infect,2012,18(12):1185-1193. |
[27] | FORSTER S C,KUMAR N,ANONYE B O,et al.A human gut bacterial genome and culture collection for improved metagenomic analyses[J].Nat Biotechnol,2019,37(2):186-192. |
[28] | LI D,WANG J Q,BU D P.Ruminal microbe of biohydrogenation of trans-vaccenic acid to stearic acid in vitro[J].BMC Res Notes, 2012,5(1):97. |
[29] | ZOU Y Q,XUE W B,LUO G W,et al.1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses[J].Nat Biotechnol,2019,37(2):179-185. |
[30] | 邢磊,赵圣国,郑楠,等.未培养微生物分离培养技术研究进展[J].微生物学通报,2017,44(12):3053-3066.XING L,ZHAO S G,ZHENG N,et al.Advance in isolation and culture techniques of uncultured microbes:a review[J].Microbiology China,2017,44(12):3053-3066.(in Chinese) |
[31] | NICHOLS D,LEWIS K,ORJALA J,et al.Short peptide induces an “uncultivable” microorganism to grow in vitro[J].Appl Environ Microbiol,2008,74(15):4889-4897. |
[32] | JALILI-FIROOZINEZHAD S,GAZZANIGA F S,CALAMARI E L,et al.A complex human gut microbiome cultured in an anaerobic intestine-on-a-chip[J].Nat Biomed Eng,2019,3(7):520-531. |
[33] | NACHTIGALL F M,PEREIRA A,TROFYMCHUK O S,et al.Detection of SARS-CoV-2 in nasal swabs using MALDI-MS[J]. Nat Biotechnol,2020,38(10):1168-1173. |
[34] | SENG P,ABAT C,ROLAIN J M,et al.Identification of rare pathogenic bacteria in a clinical microbiology laboratory:impact of matrix-assisted laser desorption ionization-time of flight mass spectrometry[J].J Clin Microbiol,2013,51(7):2182-2194. |
[35] | 张丽,徐英春.MALDI-TOF MS在临床微生物实验室的应用研究进展[J].中国感染与化疗杂志,2013,13(3):226-231.ZHANG L,XU Y C.Application of MALDI-TOF MS in clinical diagnostic microbiology[J].Chinese Journal of Infection and Chemotherapy,2013,13(3):226-231.(in Chinese) |
[36] | JOHNSON J S,SPAKOWICZ D J,HONG B Y,et al.Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis[J].Nat Commun,2019,10(1):5029. |
[37] | SANGWAN P,CHEN X L,HUGENHOLTZ P,et al.Chthoniobacter flavus gen. nov.,sp. nov.,the first pure-culture representative of subdivision two,Spartobacteria classis nov.,of the phylum Verrucomicrobia[J].Appl Environ Microbiol,2004,70(10):5875-5881. |
[38] | JAMES-HOLMQUEST A N,WENDE R D,MUDD R L,et al.Comparison of atmospheric conditions for culture of clinical specimens of Neisseria gonorrhoeae[J].Appl Environ Microbiol,1973,26(4):466-469. |
[39] | HANSEN R,BERRY S H,MUKHOPADHYA I,et al.The microaerophilic microbiota of de-novo paediatric inflammatory bowel disease:the BISCUIT study[J].PLoS One,2013,8(3):e58825. |
[40] | BROWNE H P,FORSTER S C,ANONYE B O,et al.Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation[J].Nature,2016,533(7604):543-546. |
[41] | ZHANG Z,WANG J N,WANG J L,et al.Estimate of the sequenced proportion of the global prokaryotic genome[J]. Microbiome, 2020,8(1):134. |
[42] | OBERHARDT M A,ZARECKI R,GRONOW S,et al.Harnessing the landscape of microbial culture media to predict new organism-media pairings[J].Nat Commun,2015,6(1):8493. |
[43] | HUGON P,DUFOUR J C,COLSON P,et al.A comprehensive repertoire of prokaryotic species identified in human beings[J]. Lancet Infect Dis,2015,15(10):1211-1219. |
[44] | LAGIER J C,DUBOURG G,MILLION M,et al.Culturing the human microbiota and culturomics[J].Nat Rev Microbiol,2018, 16(9):540-550. |
[45] | ZAPKA C,LEFF J,HENLEY J,et al.Comparison of standard culture-based method to culture-independent method for evaluation of hygiene effects on the hand microbiome[J].mBio,2017,8(2):e00093-17. |
[46] | LAGIER J C,KHELAIFIA S,ALOU M T,et al.Culture of previously uncultured members of the human gut microbiota by culturomics[J].Nat Microbiol,2016,1(12):16203. |
[47] | PFLEIDERER A,LAGIER J C,ARMOUGOM F,et al.Culturomics identified 11 new bacterial species from a single anorexia nervosa stool sample[J].Eur J Clin Microbiol Infect Dis,2013,32(11):1471-1481. |
[48] | LIM J W,PARK T,TONG Y W,et al.The microbiome driving anaerobic digestion and microbial analysis[J].Adv Bioenergy, 2020,5:1-61. |
[49] | DIONE N,KHELAIFIA S,LA SCOLA B,et al.A quasi-universal medium to break the aerobic/anaerobic bacterial culture dichotomy in clinical microbiology[J].Clin Microbiol Infect,2016,22(1):53-58. |
[50] | PARK T,YU Z T.Aerobic cultivation of anaerobic rumen protozoa,Entodinium caudatum and Epidinium caudatum[J].J Microbiol Methods,2018,152:186-193. |
[51] | LAGIER J C,HUGON P,KHELAIFIA S,et al.The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota[J].Clin Microbiol Rev,2015,28(1):237-264. |
[52] | HAMAD I,RANQUE S,AZHAR E I,et al.Culturomics and amplicon-based metagenomic approaches for the study of fungal population in human gut microbiota[J].Sci Rep,2017,7(1):16788. |
[53] | GOUBA N,YIMAGOU E K,HASSANI Y,et al.Enterococcus burkinafasonensis sp. nov. isolated from human gut microbiota[J].New Microbes New Infect,2020,36:100702. |
[54] | AMADOU T,HOSNY M,LA SCOLA B,et al.“Lachnoclostridium bouchesdurhonense,”a new bacterial species isolated from human gut microbiota[J].New Microbes New Infect,2016,13:69-70. |
[55] | FONKOU M M D,MAILHE M,NDONGO S,et al.Noncontiguous finished genome sequences and descriptions of Actinomyces ihuae, Actinomyces bouchesdurhonensis, Actinomyces urinae, Actinomyces marseillensis, Actinomyces mediterranea and Actinomyces oralis sp. nov. identified by culturomics[J].New Microbes New Infect,2018,25:30-44. |
[56] | VILANOVA C,PORCAR M.Are multi-omics enough?[J].Nat Microbiol,2016,1(8):16101. |
[57] | MI J D,PENG H Y,WU Y B,et al.Diversity and community of methanogens in the large intestine of finishing pigs[J].BMC Microbiol,2019,19(1):83. |
[58] | STANLEY R A,RAM S P,WILKINSON R K,et al.Degradation of pig gastric and colonic mucins by bacteria isolated from the pig colon[J].Appl Environ Microbiol,1986,51(5):1104-1109. |
[59] | LI M,WANG Y,CUI H Y,et al.Characterization of lactic acid bacteria isolated from the gastrointestinal tract of a wild boar as potential probiotics[J].Front Vet Sci,2020,7:49. |
[60] | BETANCUR C,MARTÍNEZ Y,TELLEZ-ISAIAS G,et al.In vitro characterization of indigenous probiotic strains isolated from Colombian creole pigs[J].Animals,2020,10(7):1204. |
[61] | 张锦华,余恩超,刘立恒,等.猪肠道产多肽类抗生素活性菌株的筛选与鉴定[J].黑龙江畜牧兽医,2018(17):132-135,238-239.ZHANG J H,YU E C,LIU L H,et al.Screening and identification of antimicrobial polypeptide producing bacteria from porcine intestines[J].Heilongjiang Animal Science and Veterinary Medicine,2018(17):132-135,238-239.(in Chinese) |
[62] | XU S,CHENG J J,MENG X C,et al.Complete genome and comparative genome analysis of Lactobacillus reuteri YSJL-12,a potential probiotics strain isolated from healthy sow fresh feces[J].Evol Bioinform,2020,doi:10.1177/1176934320942192. |
[63] | 黄路生,陈从英,方绍明,等.细菌在影响动物瘦肉率和/或脂肪含量中的应用:中国,201910604501.3[P].2019-11-15.HUANG L S,CHEN C Y,FANG S M,et al.Application of bacteria to influencing lean meat percentage and/or fat content of animals:CN,201910604501.3[P].2019-11-15. (in Chinese) |
[1] | 王元清, 王兢, 朱波, 陈燕, 徐凌洋, 王泽昭, 张路培, 高会江, 李俊雅, 高雪. 基因组选配研究及其在畜禽育种中的应用[J]. 畜牧兽医学报, 2024, 55(1): 1-10. |
[2] | 范定坤, 张吉贤, 付域泽, 马涛, 毕研亮, 张乃锋. 反刍动物瘤胃微生物培养组学研究进展[J]. 畜牧兽医学报, 2024, 55(1): 51-58. |
[3] | 牛乃琪, 赵润泽, 宗文成, 刘先策, 刘海, 石国华, 井西涛, 张龙超. 北京黑猪GREB1L和MIB1基因多态性与肋骨数及胴体性状的关联分析[J]. 畜牧兽医学报, 2024, 55(1): 79-86. |
[4] | 祝雪丽, 张龙超, 王立贤, 蒲蕾, 刘欣. 北京黑猪AQP9和RPS10基因多态性及其与背膘厚的关联分析[J]. 畜牧兽医学报, 2024, 55(1): 87-98. |
[5] | 时胜洁, 王立光, 高磊, 蔡传江, 何伟先, 褚瑰燕. miR-24-3p对猪颗粒细胞雌二醇合成的作用[J]. 畜牧兽医学报, 2024, 55(1): 169-178. |
[6] | 陈姝宇, 朱雪蛟, 周金柱, 陶然, 张雪寒, 索朗斯珠, 贡嘎, 李彬. 鸟苷酸结合蛋白GBP1和GBP2抑制猪轮状病毒体外复制[J]. 畜牧兽医学报, 2024, 55(1): 245-257. |
[7] | 宋雯妍, 张瀚文, 吴澳迪, 张丽燕, 刘照, 叶桐桐, 陈创夫, 盛金良. 猪繁殖与呼吸综合征病毒GP5蛋白纳米抗体的筛选及其对病毒复制的抑制效应[J]. 畜牧兽医学报, 2024, 55(1): 258-270. |
[8] | 谢青云, 邢蕙萱, 于岩飞, 袁厅, 熊祺琰, 熊富强, 冯志新. 猪肺炎支原体解螺旋酶RuvA的原核表达、多克隆抗体制备及活性鉴定[J]. 畜牧兽医学报, 2024, 55(1): 271-281. |
[9] | 白昀, 谢青云, 欧阳伟, 甘源, 袁厅, 赵东明, 步志高, 邵国青, 冯志新. 基于黏膜sIgA抗体的非洲猪瘟病毒感染早期血清学检测方法的建立[J]. 畜牧兽医学报, 2024, 55(1): 300-310. |
[10] | 马亚军, 焦智慧, 刘笑凝, 陆翔羽, 刘涛, 王月, 朴晨曦, 王洪斌. 脂肪间充质干细胞对小型猪肝缺血再灌注合并肝切除组织细胞焦亡的影响[J]. 畜牧兽医学报, 2024, 55(1): 355-364. |
[11] | 刘传霞, 王晓, 李雪雯, 鲍苗菲, 李婷婷, 陈欣, 翁长江, 郑君. 非洲猪瘟病毒pE120R蛋白单克隆抗体的制备[J]. 畜牧兽医学报, 2024, 55(1): 388-394. |
[12] | 周建浩, 王东方, 刘影, 王淑娟, 马震原, 谢彩华, 赵雪丽, 杨海波, 冯桂丹, 康台生, 胡煜锋, 李博文, 闫若潜. 猪流行性腹泻病毒微滴式数字PCR定量检测方法的建立及初步应用[J]. 畜牧兽医学报, 2024, 55(1): 413-418. |
[13] | 袁巍, 毕欢, 张雨丹, 张依裕, 顾晓龙, 杨红文, 陈伟. 全基因组选择信号解析剑白香猪和从江香猪的遗传差异[J]. 畜牧兽医学报, 2023, 54(9): 3631-3641. |
[14] | 陈莹, 钟儒清, 陈亮, 张宏福. 猪饲粮纤维的利用及其对养分消化的影响[J]. 畜牧兽医学报, 2023, 54(9): 3745-3757. |
[15] | 张兆博, 侯黎明, 李平华, 杜陶然, 王中宇, 吴承武, 黄瑞华. 基于血浆代谢组学筛选日粮纤维影响二花脸猪肉质性状的候选代谢物[J]. 畜牧兽医学报, 2023, 54(9): 3758-3769. |
阅读次数 | ||||||
全文 |
|
|||||
摘要 |
|
|||||