PLoS biology：人类肠道细菌超1000万亿

从细菌多样性程度来说，肠道堪称人体内的热带雨林。日前，发表在美国《公共科学图书馆·生物学》杂志(PLoS biology)上的一篇文章称，人类肠道内的细菌群落数量是原有认识的10倍以上。
单从数量上来说，哺乳动物结肠内的细菌群落密度堪称地球之最。人体内共有细胞约100万亿个(成年人)，细菌数量则是细胞的10倍，超过1000万亿个，而这些细菌大多集中在人类消化道中。
以前，科学家估算人体细菌种类的方法是从肠道中提取细菌，然后在培养皿上培养，待菌落长出后，再进行计数。利用这种方法得到的数据是，人体内大约有500种细菌。但这种方法有个无法弥补的缺陷：只能计算可以在培养皿中生长的常见菌落的数量，对于无法在体外环境中生长的罕见细菌，则无法计数。因此，“人体内有500种细菌”的结论并不准确。
美国斯坦福大学医学院的戴维·雷尔曼(David Relman)和同事一起，利用一种新型技术——焦磷酸测序法(pyrosequencing)，得到了关于人体肠道内菌落数量更为准确的数据。雷尔曼说：“焦磷酸测序法以前是用于评估海底环境中细菌生态系统的丰度，我们首次将这种技术用于评估人体内部的‘生态系统’。”
利用焦磷酸测序法为细菌分类时，研究人员首先要提取大量待检测细菌的DNA片段(这些片段一般编码某些常见分子)，在根据片段上的变异情况，对细菌进行分类。
论文第一作者、雷尔曼实验室的博士后研究人员雷斯·德特雷福森(Les Dethlefsen)说：“比起培养鉴别法，这种新的基因测序技术能检测到更多的细菌种类。”
雷尔曼等人发现，人体肠道内的细菌种类远超人们想象，至少有5600个细菌群落。他们的这项研究得到了美国自然科学基金会和美国国立卫生研究院的资助。
对于人体健康，肠道细菌发挥着重要作用：分解食物、微调免疫系统、分泌维生素K等营养物质、“吞”掉食物残渣……另外，细菌数量多还可以让致病菌没有立足之地。
近些年，医生为病人开的抗生素越来越多。很多科学家担心，人们经常服用抗生素类药物，会使肠道细菌数量减少，甚至可能产生更多的具有耐药性的致病菌。雷尔曼和德特雷福森希望，焦磷酸测序法进一步用于评估抗生素对肠道有益菌和人体健康的影响。（生物谷Bioon.com）
生物谷推荐原始出处：
PLoS biology，doi:10.1371/journal.pbio.0060280，Les Dethlefsen，David A. Relman
The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing
Les Dethlefsen1,2, Sue Huse3, Mitchell L. Sogin3, David A. Relman1,2,4*
1 Department of Microbiology and Immunology, Stanford University, Stanford, California, United States of America, 2 Department of Medicine, Stanford University, Stanford, California, United States of America, 3 Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America, 4 Veterans Affairs Palo Alto Health Care System, Palo Alto, California, United States of America
The human intestinal microbiota is essential to the health of the host and plays a role in nutrition, development, metabolism, pathogen resistance, and regulation of immune responses. Antibiotics may disrupt these coevolved interactions, leading to acute or chronic disease in some individuals. Our understanding of antibiotic-associated disturbance of the microbiota has been limited by the poor sensitivity, inadequate resolution, and significant cost of current research methods. The use of pyrosequencing technology to generate large numbers of 16S rDNA sequence tags circumvents these limitations and has been shown to reveal previously unexplored aspects of the “rare biosphere.” We investigated the distal gut bacterial communities of three healthy humans before and after treatment with ciprofloxacin, obtaining more than 7,000 full-length rRNA sequences and over 900,000 pyrosequencing reads from two hypervariable regions of the rRNA gene. A companion paper in PLoS Genetics (see Huse et al., doi: 10.1371/journal.pgen.1000255) shows that the taxonomic information obtained with these methods is concordant. Pyrosequencing of the V6 and V3 variable regions identified 3,300–5,700 taxa that collectively accounted for over 99% of the variable region sequence tags that could be obtained from these samples. Ciprofloxacin treatment influenced the abundance of about a third of the bacterial taxa in the gut, decreasing the taxonomic richness, diversity, and evenness of the community. However, the magnitude of this effect varied among individuals, and some taxa showed interindividual variation in the response to ciprofloxacin. While differences of community composition between individuals were the largest source of variability between samples, we found that two unrelated individuals shared a surprising degree of community similarity. In all three individuals, the taxonomic composition of the community closely resembled its pretreatment state by 4 weeks after the end of treatment, but several taxa failed to recover within 6 months. These pervasive effects of ciprofloxacin on community composition contrast with the reports by participants of normal intestinal function and with prior assumptions of only modest effects of ciprofloxacin on the intestinal microbiota. These observations support the hypothesis of functional redundancy in the human gut microbiota. The rapid return to the pretreatment community composition is indicative of factors promoting community resilience, the nature of which deserves future investigation.