Acta Veterinaria et Zootechnica Sinica ›› 2021, Vol. 52 ›› Issue (5): 1186-1194.doi: 10.11843/j.issn.0366-6964.2021.05.005
• REVIEW • Previous Articles Next Articles
ZHOU Mengqing, CHEN Congying*
Received:
2020-10-22
Online:
2021-05-23
Published:
2021-05-22
CLC Number:
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] | FAN Dingkun, ZHANG Jixian, FU Yuze, MA Tao, BI Yanliang, ZHANG Naifeng. Research Progress of Ruminant Microbial Culturomics [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(1): 51-58. |
[2] | NIU Naiqi, ZHAO Runze, ZONG Wencheng, LIU Xiance, LIU Hai, SHI Guohua, JING Xitao, ZHANG Longchao. Association of Polymorphisms of GREB1L and MIB1 Genes with Rib Number and Carcass Traits in Beijing Black Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(1): 79-86. |
[3] | ZHU Xueli, ZHANG Longchao, WANG Lixian, PU Lei, LIU Xin. Association Analysis of AQP9 and RPS10 Gene Polymorphisms with Backfat Thickness in Beijing Black Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(1): 87-98. |
[4] | SHI Shengjie, WANG Liguang, GAO Lei, CAI Chuanjiang, HE Weixian, CHU Guiyan. Effect of miR-24-3p on Estradiol Synthesis in Porcine Granulosa Cells [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(1): 169-178. |
[5] | MA Yajun, JIAO Zhihui, LIU Xiaoning, LU Xiangyu, LIU Tao, WANG Yue, PIAO Chenxi, WANG Hongbin. Effects of Adipose-derived Mesenchymal Stem Cells on Pyroptosis of Miniature Pigs with Hepatic Ischemia-Reperfusion Combined with Hepatectomy [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(1): 355-364. |
[6] | RU Meng, ZENG Wenhui, PENG Jianling, ZENG Qingjie, YIN Chao, CUI Yong, WEI Qing, LIANG Haiping, XIE Xianhua, HUANG Jianzhen. Research Progress on Follicles Development of Hens and Its Epigenetic Regulatory Mechanism [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(9): 3613-3622. |
[7] | YUAN Wei, BI Huan, ZHANG Yudan, ZHANG Yiyu, GU Xiaolong, YANG Hongwen, CHEN Wei. Deciphering Genome-wide Selection Signals Reveals Genetic Differences between Jianbai and Congjiang Xiang Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(9): 3631-3641. |
[8] | CHEN Ying, ZHONG Ruqing, CHEN Liang, ZHANG Hongfu. Utilization of Dietary Fiber and Its Impact on Nutrient Digestion of Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(9): 3745-3757. |
[9] | ZHANG Zhaobo, HOU Liming, LI Pinghua, DU Taoran, WANG Zhongyu, WU Chengwu, HUANG Ruihua. Screening Candidate Metabolites of Dietary Fiber Affecting Meat Quality Traits of Erhualian Pigs Based on Plasma Metabolomics [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(9): 3758-3769. |
[10] | ZHENG Xianrui, ZHUO Mingxue, JI Jinli, JIANG Weihu, DENG Zaishuang, ZHANG Jicheng, TIAN Yali, DING Yueyun, ZHANG Xiaodong, YIN Zongjun. Characteristics of Serum Immune Indices and Intestinal Microbiota of Wannan Black Pigs at Different Growth Stages [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(9): 3770-3783. |
[11] | FAN Yandi, YANG Danjiao, YE Zhongming, ZHANG Min, LAN Lan, WANG Jinghao, ZHOU Han, KANG Runmin, YU Jifeng, ZHANG Zhidong, LI Yanmin, ZHOU Long. Metagenomic Analysis of Viruses in Clinical Samples of Respiratory Diseases in Tibetan Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(9): 3836-3847. |
[12] | LIANG Rui, FAN Xiaorui, ZHANG Jinqiang, PANG Quanhai. Effects of Mouse Melanocyte Silencing and Overexpression of Pigment Epithelium-Derived Factor on Melanin Synthesis [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(9): 3916-3930. |
[13] | JIAO Guangming, LÜ Yingguang, SANG Jinfang, KOU Zhipeng, LIU Tao, WANG Yue, LU Xiangyu, PIAO Chenxi, MA Yajun, ZHANG Jiantao, WANG Hongbin. Effect of Adipose Mesenchymal Stem Cells in Combination with Methylprednisolone on Allogeneic Skin Grafts in Minipigs [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(8): 3533-3545. |
[14] | LIAN Yuju, ZHANG Zhiyuan, LIAO Xiaobo, WEI Hongjiang, YIN Yulong, LIU Mei. Breeding Methods and Application Progress of Medical Miniature Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(7): 2667-2682. |
[15] | LU Chang, DONG Lei, ZHANG Wanfeng, GAO Pengfei, GUO Xiaohong, CAI Chunbo, CAO Guoqing, LI Bugao. Identification and Screening of Single Nucleotide Polymorphism Loci in Jinfen White Pigs Based on Whole Genome Resequencing [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(7): 2761-2771. |
Viewed | ||||||
Full text |
|
|||||
Abstract |
|
|||||