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《Trends in microbiology》2023,31(4):356-368
The vaginal microbiome (VMB) is critical to female reproductive health; however, the mechanisms associated with optimal and non-optimal states remain poorly understood due to the complex community structure and dynamic nature. Quantitative systems biology techniques applied to the VMB have improved understanding of community composition and function using primarily statistical methods. In contrast, fewer mechanistic models that use a priori knowledge of VMB features to develop predictive models have been implemented despite their use for microbiomes at other sites, including the gastrointestinal tract. Here, we explore systems biology approaches that have been applied in the VMB, highlighting successful techniques and discussing new directions that hold promise for improving understanding of health and disease. 相似文献
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Caporaso JG Lauber CL Costello EK Berg-Lyons D Gonzalez A Stombaugh J Knights D Gajer P Ravel J Fierer N Gordon JI Knight R 《Genome biology》2011,12(5):R50-8
Background
Understanding the normal temporal variation in the human microbiome is critical to developing treatments for putative microbiome-related afflictions such as obesity, Crohn's disease, inflammatory bowel disease and malnutrition. Sequencing and computational technologies, however, have been a limiting factor in performing dense time series analysis of the human microbiome. Here, we present the largest human microbiota time series analysis to date, covering two individuals at four body sites over 396 timepoints.Results
We find that despite stable differences between body sites and individuals, there is pronounced variability in an individual's microbiota across months, weeks and even days. Additionally, only a small fraction of the total taxa found within a single body site appear to be present across all time points, suggesting that no core temporal microbiome exists at high abundance (although some microbes may be present but drop below the detection threshold). Many more taxa appear to be persistent but non-permanent community members.Conclusions
DNA sequencing and computational advances described here provide the ability to go beyond infrequent snapshots of our human-associated microbial ecology to high-resolution assessments of temporal variations over protracted periods, within and between body habitats and individuals. This capacity will allow us to define normal variation and pathologic states, and assess responses to therapeutic interventions. 相似文献10.
Until recently, bacterial species that inhabit the human vagina have been primarily studied using organism-centric approaches. Understanding how these bacterial species interact with each other and the host vaginal epithelium is essential for a more complete understanding of vaginal health. Molecular approaches have already led to the identification of uncultivated bacterial taxa associated with bacterial vaginosis. Here, we review recent studies of the vaginal microbiome and discuss how culture-independent approaches, such as applications of next-generation sequencing, are advancing the field and shifting our understanding of how vaginal health is defined. This work may lead to improved diagnostic tools and treatments for women who suffer from, or are at risk for, vaginal imbalances, pregnancy complications, and sexually acquired infections. These approaches may also transform our understanding of how host genetic factors, physiological conditions (e.g., menopause), and environmental exposures (e.g., smoking, antibiotic usage) influence the vaginal microbiome. 相似文献
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Aagaard K Riehle K Ma J Segata N Mistretta TA Coarfa C Raza S Rosenbaum S Van den Veyver I Milosavljevic A Gevers D Huttenhower C Petrosino J Versalovic J 《PloS one》2012,7(6):e36466
While current major national research efforts (i.e., the NIH Human Microbiome Project) will enable comprehensive metagenomic characterization of the adult human microbiota, how and when these diverse microbial communities take up residence in the host and during reproductive life are unexplored at a population level. Because microbial abundance and diversity might differ in pregnancy, we sought to generate comparative metagenomic signatures across gestational age strata. DNA was isolated from the vagina (introitus, posterior fornix, midvagina) and the V5V3 region of bacterial 16S rRNA genes were sequenced (454FLX Titanium platform). Sixty-eight samples from 24 healthy gravidae (18 to 40 confirmed weeks) were compared with 301 non-pregnant controls (60 subjects). Generated sequence data were quality filtered, taxonomically binned, normalized, and organized by phylogeny and into operational taxonomic units (OTU); principal coordinates analysis (PCoA) of the resultant beta diversity measures were used for visualization and analysis in association with sample clinical metadata. Altogether, 1.4 gigabytes of data containing >2.5 million reads (averaging 6,837 sequences/sample of 493 nt in length) were generated for computational analyses. Although gravidae were not excluded by virtue of a posterior fornix pH >4.5 at the time of screening, unique vaginal microbiome signature encompassing several specific OTUs and higher-level clades was nevertheless observed and confirmed using a combination of phylogenetic, non-phylogenetic, supervised, and unsupervised approaches. Both overall diversity and richness were reduced in pregnancy, with dominance of Lactobacillus species (L. iners crispatus, jensenii and johnsonii, and the orders Lactobacillales (and Lactobacillaceae family), Clostridiales, Bacteroidales, and Actinomycetales. This intergroup comparison using rigorous standardized sampling protocols and analytical methodologies provides robust initial evidence that the vaginal microbial 16S rRNA gene catalogue uniquely differs in pregnancy, with variance of taxa across vaginal subsite and gestational age. 相似文献
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人体微生物组计划又称第二人类基因组计划。由美国国立卫生研究院立项资助,2007年正式启动。计划用5年时间耗资1.5亿美元完成900个人体微生物基因组测序。其目标是探索研究人类微生物组的可行性;研究人体微生物组变化与疾病健康的关系;同时为其它科学研究提供信息和技术支持。 相似文献
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Multiple factors drive the progression from healthy mucosa towards sporadic colorectal carcinomas and accumulating evidence associates intestinal bacteria with disease initiation and progression. Therefore, the aim of this study was to provide a first high-resolution map of colonic dysbiosis that is associated with human colorectal cancer (CRC). To this purpose, the microbiomes colonizing colon tumor tissue and adjacent non-malignant mucosa were compared by deep rRNA sequencing. The results revealed striking differences in microbial colonization patterns between these two sites. Although inter-individual colonization in CRC patients was variable, tumors consistently formed a niche for Coriobacteria and other proposed probiotic bacterial species, while potentially pathogenic Enterobacteria were underrepresented in tumor tissue. As the intestinal microbiota is generally stable during adult life, these findings suggest that CRC-associated physiological and metabolic changes recruit tumor-foraging commensal-like bacteria. These microbes thus have an apparent competitive advantage in the tumor microenvironment and thereby seem to replace pathogenic bacteria that may be implicated in CRC etiology. This first glimpse of the CRC microbiome provides an important step towards full understanding of the dynamic interplay between intestinal microbial ecology and sporadic CRC, which may provide important leads towards novel microbiome-related diagnostic tools and therapeutic interventions. 相似文献
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分析不同妊娠结局女性孕晚期阴道菌群,探索阴道菌群变化与妊娠结局的相关性。
收集厦门市第五医院收治的妊娠期女性阴道分泌物,筛选排除后,纳入不良妊娠组14例,正常妊娠组17例。采用高通量测序法对阴道菌群16S rDNA V3−V4区进行测序;采用QIIME2软件分析阴道菌群的组成和多样性指标;采用PCoA主坐标分析菌群β多样性差异;采用LEfSe比较不同妊娠结局女性阴道微生物差异,获得具有统计学意义的菌群标志物,并对差异菌群做相关性分析。
在菌群组成方面,厚壁菌门、乳杆菌属比例在正常妊娠组中显著增加,放线菌门、双歧杆菌属比例在不良妊娠组中显著升高(均
与正常妊娠组相比,不良妊娠组女性阴道菌群存在多样性下降、乳杆菌丰度下降的趋势,同时双歧杆菌、加德纳菌、梭菌等厌氧菌丰度增加。
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Zhanshan Ma 《Molecular ecology》2015,24(21):5428-5445
Taylor's (1961, Nature, 189:732) power law, a power function (V = amb) describing the scaling relationship between the mean and variance of population abundances of organisms, has been found to govern the population abundance distributions of single species in both space and time in macroecology. It is regarded as one of few generalities in ecology, and its parameter b has been widely applied to characterize spatial aggregation (i.e. heterogeneity) and temporal stability of single‐species populations. Here, we test its applicability to bacterial populations in the human microbiome using extensive data sets generated by the US‐NIH Human Microbiome Project (HMP). We further propose extending Taylor's power law from the population to the community level, and accordingly introduce four types of power‐law extensions (PLEs): type I PLE for community spatial aggregation (heterogeneity), type II PLE for community temporal aggregation (stability), type III PLE for mixed‐species population spatial aggregation (heterogeneity) and type IV PLE for mixed‐species population temporal aggregation (stability). Our results show that fittings to the four PLEs with HMP data were statistically extremely significant and their parameters are ecologically sound, hence confirming the validity of the power law at both the population and community levels. These findings not only provide a powerful tool to characterize the aggregations of population and community in both time and space, offering important insights into community heterogeneity in space and/or stability in time, but also underscore the three general properties of power laws (scale invariance, no average and universality) and their specific manifestations in our four PLEs. 相似文献