Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture.
Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture.
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作者：
Gilroy R;Ravi A;Getino M;Pursley I;Horton DL;Alikhan NF;Baker D;Gharbi K;Hall N;Watson M;Adriaenssens EM;Foster-Nyarko E;Jarju S;Secka A;Antonio M;Oren A;Chaudhuri RR;La Ragione R;Hildebrand F;Pallen MJ
鸡是世界上最丰富的食用动物。然而，尽管它很重要，但鸡肠道微生物群在很大程度上仍未被定义。在这里，我们利用培养独立和培养依赖的方法来揭示这个复杂的微生物群落中广泛的分类多样性。我们对来自两个品种的50份鸡粪便样本进行了宏基因组测序，并分析了这些样本以及所有相关的公开鸡宏基因组（n = 582），聚类了超过2000万个非冗余基因，构建了超过5500个宏基因组组装的细菌基因组。此外，我们回收了近600个噬菌体基因组。这代表了迄今为止鸡肠道微生物组中最全面的分类多样性观点，包括数百种新的候选细菌属和物种。为了给新物种提供一个稳定、清晰和令人难忘的命名，我们设计了一个可扩展的组合系统，用于创建数百个结构良好的拉丁二项式。我们对从鸡粪便中分离出来的细菌进行了培养和基因组测序，记录了40多种新种，包括3种埃希氏菌属，包括新命名的惠塔米埃希氏菌。我们的宏基因组和基于培养的分析为鸡肠道微生物组的细菌、古细菌和噬菌体成分提供了新的见解。由此产生的数据集扩展了已知的鸡肠道微生物组的多样性，并为未来鸡肠道微生物组的高分辨率分类和功能研究提供了关键资源。
The chicken is the most abundant food animal in the world. However, despite its importance, the chicken gut microbiome remains largely undefined. Here, we exploit culture-independent and culture-dependent approaches to reveal extensive taxonomic diversity within this complex microbial community. We performed metagenomic sequencing of fifty chicken faecal samples from two breeds and analysed these, alongside all (n = 582) relevant publicly available chicken metagenomes, to cluster over 20 million non-redundant genes and to construct over 5,500 metagenome-assembled bacterial genomes. In addition, we recovered nearly 600 bacteriophage genomes. This represents the most comprehensive view of taxonomic diversity within the chicken gut microbiome to date, encompassing hundreds of novel candidate bacterial genera and species. To provide a stable, clear and memorable nomenclature for novel species, we devised a scalable combinatorial system for the creation of hundreds of well-formed Latin binomials. We cultured and genome-sequenced bacterial isolates from chicken faeces, documenting over forty novel species, together with three species from the genus Escherichia, including the newly named species Escherichia whittamii. Our metagenomic and culture-based analyses provide new insights into the bacterial, archaeal and bacteriophage components of the chicken gut microbiome. The resulting datasets expand the known diversity of the chicken gut microbiome and provide a key resource for future high-resolution taxonomic and functional studies on the chicken gut microbiome.
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影响因子：
3.9
作者：
Connor TR;Loman NJ;Thompson S;Smith A;Southgate J;Poplawski R;Bull MJ;Richardson E;Ismail M;Thompson SE;Kitchen C;Guest M;Bakke M;Sheppard SK;Pallen MJ
通讯作者：
Pallen MJ
DOI：
10.1093/bioinformatics/bts565
发表时间：
2012-12-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Fu L;Niu B;Zhu Z;Wu S;Li W
通讯作者：
Li W
影响因子：
5.1
作者：
Clermont, Olivier;Gordon, David M.;Denamur, Erick
通讯作者：
Denamur, Erick
影响因子：
--
作者：
Florez-Cuadrado, Diego;Moreno, Miguel A;Dominguez, Lucas
通讯作者：
Dominguez, Lucas
DOI：
10.1099/ijs.0.058545-0
发表时间：
2014-06-01
影响因子：
2.8
作者：
Amoozegar, Mohammad Ali;Bagheri, Maryam;Ventosa, Antonio
通讯作者：
Ventosa, Antonio