Microbial diversity and community composition of caecal microbiota in commercial and indigenous Indian chickens determined using 16s rDNA amplicon sequencing.
Microbial diversity and community composition of caecal microbiota in commercial and indigenous Indian chickens determined using 16s rDNA amplicon sequencing.
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DOI：
10.1186/s40168-018-0501-9
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发表时间：
2018-06-23
期刊：
影响因子：
15.5
通讯作者：
Joshi CG
中科院分区：
文献类型：
--
作者：
Pandit RJ;Hinsu AT;Patel NV;Koringa PG;Jakhesara SJ;Thakkar JR;Shah TM;Limon G;Psifidi A;Guitian J;Hume DA;Tomley FM;Rank DN;Raman M;Tirumurugaan KG;Blake DP;Joshi CG
盲肠微生物群在鸡的健康和生产性能中起着关键作用，影响营养物质的消化和吸收，并有助于防御入侵病原体的定植。鸡的生产力和对病原体定植的抗性直接受到鸡基因型的影响，但宿主驱动的微生物组结构变异也可能产生相当大的间接影响。本研究利用16S rDNA V3-V4高变扩增子测序技术，确定了印度本土asiel和Kadaknath鸡品种的盲肠微生物群，并将其与全球商品肉鸡Cobb400和Ross 308进行了比较。盲肠各菌群以拟杆菌属、未分类细菌、未分类梭状芽孢杆菌属、梭状芽孢杆菌属、Alistipes、Faecalibacterium、Eubacterium和Blautia为主。地理位置（一种被认为包括环境和气候因素变化的措施，但也可能包括不同的管理措施）和鸡系/品种都被发现对盲肠微生物组组成产生显著影响（p < 0.05）。线性判别分析效应大小（LEfSe）揭示了在两个不同地点控制条件下饲养的鸡系中42个品种特异性生物标志物。细菌发生的鸡种特异性差异、属间的相关性和操作分类单位的聚类表明了定量遗传分析的范围和对特定肠道微生物群的鸡进行选择性育种的可能性。本文的在线版本（10.1186/s40168-018-0501-9）包含补充材料，可供授权用户使用。
The caecal microbiota plays a key role in chicken health and performance, influencing digestion and absorption of nutrients, and contributing to defence against colonisation by invading pathogens. Measures of productivity and resistance to pathogen colonisation are directly influenced by chicken genotype, but host driven variation in microbiome structure is also likely to exert a considerable indirect influence. Here, we define the caecal microbiome of indigenous Indian Aseel and Kadaknath chicken breeds and compare them with the global commercial broiler Cobb400 and Ross 308 lines using 16S rDNA V3-V4 hypervariable amplicon sequencing. Each caecal microbiome was dominated by the genera Bacteroides, unclassified bacteria, unclassified Clostridiales, Clostridium, Alistipes, Faecalibacterium, Eubacterium and Blautia. Geographic location (a measure recognised to include variation in environmental and climatic factors, but also likely to feature varied management practices) and chicken line/breed were both found to exert significant impacts (p < 0.05) on caecal microbiome composition. Linear discriminant analysis effect size (LEfSe) revealed 42 breed-specific biomarkers in the chicken lines reared under controlled conditions at two different locations. Chicken breed-specific variation in bacterial occurrence, correlation between genera and clustering of operational taxonomic units indicate scope for quantitative genetic analysis and the possibility of selective breeding of chickens for defined enteric microbiota. The online version of this article (10.1186/s40168-018-0501-9) contains supplementary material, which is available to authorized users.
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影响因子：
14.9
作者：
Klindworth A;Pruesse E;Schweer T;Peplies J;Quast C;Horn M;Glöckner FO
通讯作者：
Glöckner FO
影响因子：
2.6
作者：
Jung A;Rautenschlein S
通讯作者：
Rautenschlein S
影响因子：
14.9
作者：
Arndt D;Xia J;Liu Y;Zhou Y;Guo AC;Cruz JA;Sinelnikov I;Budwill K;Nesbø CL;Wishart DS
通讯作者：
Wishart DS
影响因子：
4.4
作者：
Lu, JR;Idris, U;Lee, MD
通讯作者：
Lee, MD
DOI：
10.1073/pnas.0504978102
发表时间：
2005-08-02
影响因子：
11.1
作者：
Ley, RE;Bäckhed, F;Gordon, JI
通讯作者：
Gordon, JI