Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents.
Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents.
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DOI：
10.1371/journal.pone.0066019
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Bushman FD
中科院分区：
文献类型：
--
作者：
Hoffmann C;Dollive S;Grunberg S;Chen J;Li H;Wu GD;Lewis JD;Bushman FD
饮食作为营养素和毒素的来源，并通过塑造常驻微生物种群的组成来影响健康。以前的研究已经开始绘制饮食与人类肠道微生物组的细菌和病毒之间的关联。在这里，我们调查协会的饮食与真菌和古菌种群，利用样本从98个特征良好的个人。使用对长期和近期饮食进行评分的库存来量化饮食，并通过对从粪便中纯化的DNA中的标记基因进行深度测序来表征古细菌和真菌。对于真菌，我们发现了66个属，通常相互排斥的存在无论是子囊菌门或Basiodiomycota。对于古菌，甲烷短杆菌是最普遍的属，存在于30%的样品中。其他几个古菌属的丰度和频率较低。真菌和古菌与饮食、彼此之间以及与细菌谱系之间存在着无数的关联。甲烷短杆菌和念珠菌与高碳水化合物饮食呈正相关，但与高氨基酸、蛋白质和脂肪酸饮食呈负相关。先前的一项研究强调，细菌种群结构主要与长期饮食有关，但高念珠菌丰度与最近的碳水化合物消费密切相关。甲烷短杆菌的丰度与长期和近期的碳水化合物消费有关。这些结果证实了早期的有针对性的研究，并提供了一系列新的关联，以考虑饮食对肠道微生物组和人类健康的影响。
Diet influences health as a source of nutrients and toxins, and by shaping the composition of resident microbial populations. Previous studies have begun to map out associations between diet and the bacteria and viruses of the human gut microbiome. Here we investigate associations of diet with fungal and archaeal populations, taking advantage of samples from 98 well-characterized individuals. Diet was quantified using inventories scoring both long-term and recent diet, and archaea and fungi were characterized by deep sequencing of marker genes in DNA purified from stool. For fungi, we found 66 genera, with generally mutually exclusive presence of either the phyla Ascomycota or Basiodiomycota. For archaea, Methanobrevibacter was the most prevalent genus, present in 30% of samples. Several other archaeal genera were detected in lower abundance and frequency. Myriad associations were detected for fungi and archaea with diet, with each other, and with bacterial lineages. Methanobrevibacter and Candida were positively associated with diets high in carbohydrates, but negatively with diets high in amino acids, protein, and fatty acids. A previous study emphasized that bacterial population structure was associated primarily with long-term diet, but high Candida abundance was most strongly associated with the recent consumption of carbohydrates. Methobrevibacter abundance was associated with both long term and recent consumption of carbohydrates. These results confirm earlier targeted studies and provide a host of new associations to consider in modeling the effects of diet on the gut microbiome and human health.
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使用通用的unifrac距离将微生物组组成与环境协变量相关联。
DOI：
10.1093/bioinformatics/bts342
发表时间：
2012-08-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Chen J;Bittinger K;Charlson ES;Hoffmann C;Lewis J;Wu GD;Collman RG;Bushman FD;Li H
通讯作者：
Li H
DOI：
10.1126/science.1224203
发表时间：
2012-06-08
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Costello EK;Stagaman K;Dethlefsen L;Bohannan BJ;Relman DA
通讯作者：
Relman DA
影响因子：
4.3
作者：
Faust K;Sathirapongsasuti JF;Izard J;Segata N;Gevers D;Raes J;Huttenhower C
通讯作者：
Huttenhower C
影响因子：
64.8
作者：
Arumugam, Manimozhiyan;Raes, Jeroen;Pelletier, Eric;Le Paslier, Denis;Yamada, Takuji;Mende, Daniel R.;Fernandes, Gabriel R.;Tap, Julien;Bruls, Thomas;Batto, Jean-Michel;Bertalan, Marcelo;Borruel, Natalia;Casellas, Francesc;Fernandez, Leyden;Gautier, Laurent;Hansen, Torben;Hattori, Masahira;Hayashi, Tetsuya;Kleerebezem, Michiel;Kurokawa, Ken;Leclerc, Marion;Levenez, Florence;Manichanh, Chaysavanh;Nielsen, H. Bjorn;Nielsen, Trine;Pons, Nicolas;Poulain, Julie;Qin, Junjie;Sicheritz-Ponten, Thomas;Tims, Sebastian;Torrents, David;Ugarte, Edgardo;Zoetendal, Erwin G.;Wang, Jun;Guarner, Francisco;Pedersen, Oluf;de Vos, Willem M.;Brunak, Soren;Dore, Joel;Weissenbach, Jean;Ehrlich, S. Dusko;Bork, Peer
通讯作者：
Bork, Peer
影响因子：
56.9
作者：
Gill, Steven R.;Pop, Mihai;Nelson, Karen E.
通讯作者：
Nelson, Karen E.