The Earth Microbiome Project: Meeting report of the "1 EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 2010

This report details the outcome the first meeting of the Earth Microbiome Project to discuss sample selection and acquisition. The meeting, held at the Argonne National Laboratory on Wednesday October 6(th) 2010, focused on discussion of how to prioritize environmental samples for sequencing and metagenomic analysis as part of the global effort of the EMP to systematically determine the functional and phylogenetic diversity of microbial communities across the world.     

The Human Microbiome Project in 2011 and beyond

The human microbiome comprises the genes and genomes of the microbiota that inhabit the body. We highlight Human Microbiome Project (HMP) resources, including 600 microbial reference genomes, 70 million 16S sequences, 700 metagenomes, and 60 million predicted genes from healthy adult microbiomes. Microbiome studies of specific diseases and future research directions are also discussed.     

The Human Microbiome Project: lessons from human genomics

The Human Microbiome Project (HMP) is following in the footsteps of the Human Genome Project (HGP), which will include exciting discoveries, but also potential disappointment and resentment over the lack of medical applications. There is a wiser path for the HMP. This path includes a greater attention to rare variation, an early commitment to an ethical inclusion of indigenous communities, and a recruitment strategy in which medical benefits are de-emphasized.     

The Hospital Microbiome Project: Meeting Report for the 1st Hospital Microbiome Project Workshop on sampling design and building science measurements,Chicago, USA,June 7th-8th 2012

This report details the outcome of the 1st Hospital Microbiome Project workshop held on June 7th-8th, 2012 at the University of Chicago, USA. The workshop was arranged to determine the most appropriate sampling strategy and approach to building science measurement to characterize the development of a microbial community within a new hospital pavilion being built at the University of Chicago Medical Center. The workshop made several recommendations and led to the development of a full proposal to the Alfred P. Sloan Foundation as well as to the creation of the Hospital Microbiome Consortium.     

Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project

Between July 18(th) and 24(th) 2010, 26 leading microbial ecology, computation, bioinformatics and statistics researchers came together in Snowbird, Utah (USA) to discuss the challenge of how to best characterize the microbial world using next-generation sequencing technologies. The meeting was entitled "Terabase Metagenomics" and was sponsored by the Institute for Computing in Science (ICiS) summer 2010 workshop program. The aim of the workshop was to explore the fundamental questions relating to microbial ecology that could be addressed using advances in sequencing potential. Technological advances in next-generation sequencing platforms such as the Illumina HiSeq 2000 can generate in excess of 250 billion base pairs of genetic information in 8 days. Thus, the generation of a trillion base pairs of genetic information is becoming a routine matter. The main outcome from this meeting was the birth of a concept and practical approach to exploring microbial life on earth, the Earth Microbiome Project (EMP). Here we briefly describe the highlights of this meeting and provide an overview of the EMP concept and how it can be applied to exploration of the microbiome of each ecosystem on this planet.     

微生物组大数据管理与分析

高通量技术的迅猛发展促使微生物生态学研究获得了重大突破,掀起了元基因组学(Metagenomics)研究的热潮。元基因组学通常被定义为对未培养的环境样本中微生物群体的DNA序列分析。随着微生物组学数据的日益剧增,微生物大数据的高效管理与分析越来越受到研究者的关注。如何从海量的微生物组数据中挖掘出具有科研价值的数据信息并应用于实际问题成为当前的研究热点。目前已有很多计算生物学程序工具及数据库用于元基因组数据的分析与管理。本文主要综述了随着高通量测序技术的进步,国际上主要的微生物组计划及微生物组数据平台,如人类微生物组项目(human microbiome project,HMP)、地球微生物组项目(earth microbiome project,EMP)、欧盟的肠道微生物组计划(metagenomics of human intestinal tract,MetaHIT)、MG-RAST、i Microbe、整合微生物组(integration microbial genomes,IMG)以及EBI Metagenomics等;介绍了微生物数据分析的主要流程与工具;提出了建设多源异构的微生物生态数据管理与分析系统的必要性。     

The Microbiome of the Middle Meatus in Healthy Adults

Rhinitis and rhinosinusitis are multifactorial disease processes in which bacteria may play a role either in infection or stimulation of the inflammatory process. Rhinosinusitis has been historically studied with culture-based techniques, which have implicated several common pathogens in disease states. More recently, the NIH Human Microbiome Project has examined the microbiome at a number of accessible body sites, and demonstrated differences among healthy and diseased patients. Recent DNA-based sinus studies have suggested that healthy sinuses are not sterile, as was previously believed, but the normal sinonasal microbiome has yet to be thoroughly examined. Middle meatus swab specimens were collected from 28 consecutive patients presenting with no signs or symptoms of rhinosinusitis. Bacterial colonization was assessed in these specimens using quantitative PCR and 16S rRNA pyrosequencing. All subjects were positive for bacterial colonization of the middle meatus. Staphylococcus aureus, Staphylococcus epidermidis and Propionibacterium acnes were the most prevalent and abundant microorganisms detected. Rich and diverse bacterial assemblages are present in the sinonasal cavity in the normal state, including opportunistic pathogens typically found in the nasopharynx. This work helps establish a baseline for understanding how the sinonasal microbiome may impact diseases of the upper airways.     

Focus: Microbiome: The Influence of the Gut Microbiota on Host Physiology: In Pursuit of Mechanisms

The results generated from the NIH funded Human Microbiome Project (HMP) are necessarily tied to the overall mission of the agency, which is to foster scientific discoveries as a basis for protecting and improving health. The investment in the HMP phase 1 accomplished many of its goals including the preliminary characterization of the human microbiome and the identification of links between microbiome diversity and disease states. Going forward, the next step in these studies must involve the identification of the functional molecular elements that mediate the positive influence of a eubiotic microbiome on health and disease. This review will focus on recent advances describing mechanistic events in the intestine elicited by the microbiome. These include symbiotic bacteria-induced activation of redox-dependent cell signaling, the bacterial production of short chain fatty acids and ensuing cellular responses, and the secretion of bacteriocins by bacteria that have anti-microbial activities against potential pathogens.     

The Prevalence of Species and Strains in the Human Microbiome: A Resource for Experimental Efforts

Experimental efforts to characterize the human microbiota often use bacterial strains that were chosen for historical rather than biological reasons. Here, we report an analysis of 380 whole-genome shotgun samples from 100 subjects from the NIH Human Microbiome Project. By mapping their reads to 1,751 reference genome sequences and analyzing the resulting relative strain abundance in each sample we present metrics and visualizations that can help identify strains of interest for experimentalists. We also show that approximately 14 strains of 10 species account for 80% of the mapped reads from a typical stool sample, indicating that the function of a community may not be irreducibly complex. Some of these strains account for >20% of the sequence reads in a subset of samples but are absent in others, a dichotomy that could underlie biological differences among subjects. These data should serve as an important strain selection resource for the community of researchers who take experimental approaches to studying the human microbiota.     

Megafauna in the Earth system

Understanding the complex role of large‐bodied mammals in contemporary ecosystems and the likely consequences of their continued decline is essential for effective management of the remaining wild areas on Earth. The very largest animals are in particular peril owing to a disastrous combination of continued hunting or poaching, habitat alterations, and loss of habitat. Because these threats are ongoing, conservation biologists may not be able to wait for the results of long‐term studies before proposing potential mitigation strategies. A recent conference on ‘Megafauna and ecosystem function: from the Pleistocene to the Anthropocene’ at Oxford Univ. brought together paleontologists, conservation and environmental scientists and others who share an interest in characterizing the influence of large animals on ecosystems. Integrating historical perspectives of Late Pleistocene ecosystems when large‐bodied animals were still widespread, with modern studies of areas with varying levels of intact megafauna, the aim was to develop a more holistic understanding of the consequences of the ongoing decline of large‐bodied animals around the Earth. The conference resulted in the development of two special features – one in the Proceedings of the National Academy of Science, USA and one in Ecography synthesizing the state of our knowledge about the environmental legacies of the terminal Pleistocene megafauna extinction, the complex role of modern large‐bodied animals and what the ongoing loss of their ecological interactions might mean in terms of ecosystem function. Here, we briefly review the main themes developed during the conference and outline promising future research directions.     

The Plate Tectonics Project

The Plate Tectonics Project is a multiday, inquiry-based unit that facilitates students as self-motivated learners. Reliable Web sites are offered to assist with lessons, and a summative rubric is used to facilitate the holistic nature of the project. After each topic (parts of the Earth, continental drift, etc.) is covered, the students will generate a portion of the summative assessment that will be set aside and later compiled into a booklet. This summative assessment creates the circumstance in which each student must develop literacy and organizational skills to master the concept that the Earth is a global, dynamic, lithospheric system.     

Estimate of the degradation potentials of cellulose,xylan, and chitin across global prokaryotic communities

Complex polysaccharides (e.g. cellulose, xylan, and chitin), the most abundant renewable biomass resources available on Earth, are mainly degraded by microorganisms in nature. However, little is known about the global distribution of the enzymes and microorganisms responsible for the degradation of cellulose, xylan, and chitin in natural environments. Through large-scale alignments between the sequences released by the Earth Microbiome Project and sequenced prokaryotic genomes, we determined that almost all prokaryotic communities have the functional potentials to degrade cellulose, xylan, and chitin. The median abundances of genes encoding putative cellulases, xylanases, and chitinases in global prokaryotic communities are 0.51 (0.17–1.01), 0.24 (0.05–0.57), and 0.33 (0.11–0.71) genes/cell, respectively, and the composition and abundance of these enzyme systems are environmentally varied. The taxonomic sources of the three enzymes are highly diverse within prokaryotic communities, and the main factor influencing the diversity is the community's alpha diversity index rather than gene abundance. Moreover, there are obvious differences in taxonomic sources among different communities, and most genera with degradation potentials are narrowly distributed. In conclusion, our analysis preliminarily depicts a panorama of cellulose-, xylan-, and chitin-degrading enzymatic systems across global prokaryotic communities.     

Societal and Medical Consequences of the Human Genome Project

The Human Genome Project is a US-based molecular biological project, the results of which are likely to be implemented on humans. The sociopolitical dimension of this is highly neglected. The aim of the conference was to fill this gap by drawing together scientists of natural and political sciences to discuss the consequences of the Human Genome Project across the disciplines.     

Functional Environmental Screening of a Metagenomic Library Identifies stlA; A Unique Salt Tolerance Locus from the Human Gut Microbiome

Functional environmental screening of metagenomic libraries is a powerful means to identify and assign function to novel genes and their encoded proteins without any prior sequence knowledge. In the current study we describe the identification and subsequent analysis of a salt-tolerant clone from a human gut metagenomic library. Following transposon mutagenesis we identified an unknown gene (stlA, for “salt tolerance locus A”) with no current known homologues in the databases. Subsequent cloning and expression in Escherichia coli MKH13 revealed that stlA confers a salt tolerance phenotype in its surrogate host. Furthermore, a detailed in silico analysis was also conducted to gain additional information on the properties of the encoded StlA protein. The stlA gene is rare when searched against human metagenome datasets such as MetaHit and the Human Microbiome Project and represents a novel and unique salt tolerance determinant which appears to be found exclusively in the human gut environment.     

Evaluation of Microbiome Alterations Following Consumption of BIOHM,a Novel Probiotic

Gastrointestinal microbiome dysbiosis may result in harmful effects on the host, including those caused by inflammatory bowel diseases (IBD). The novel probiotic BIOHM, consisting of Bifidobacterium breve, Saccharomyces boulardii, Lactobacillus acidophilus, L. rhamnosus, and amylase, was developed to rebalance the bacterial–fungal gut microbiome, with the goal of reducing inflammation and maintaining a healthy gut population. To test the effect of BIOHM on human subjects, we enrolled a cohort of 49 volunteers in collaboration with the Fermentation Festival group (Santa Barbara, CA, USA). The profiles of gut bacterial and fungal communities were assessed via stool samples collected at baseline and following 4 weeks of once-a-day BIOHM consumption. Mycobiome analysis following probiotic consumption revealed an increase in Ascomycota levels in enrolled individuals and a reduction in Zygomycota levels (p value < 0.01). No statistically significant difference in Basidiomycota was detected between pre- and post-BIOHM samples and control abundance profiles (p > 0.05). BIOHM consumption led to a significant reduction in the abundance of Candida genus in tested subjects (p value < 0.013), while the abundance of C. albicans also trended lower than before BIOHM use, albeit not reaching statistical significance. A reduction in the abundance of Firmicutes at the phylum level was observed following BIOHM use, which approached levels reported for control individuals reported in the Human Microbiome Project data. The preliminary results from this clinical study suggest that BIOHM is capable of significantly rebalancing the bacteriome and mycobiome in the gut of healthy individuals, suggesting that further trials examining the utility of the BIOHM probiotic in individuals with gastrointestinal symptoms, where dysbiosis is considered a source driving pathogenesis, are warranted.     

人体微生物组计划

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。     

Evaluation of 16S rDNA-based community profiling for human microbiome research

The Human Microbiome Project will establish a reference data set for analysis of the microbiome of healthy adults by surveying multiple body sites from 300 people and generating data from over 12,000 samples. To characterize these samples, the participating sequencing centers evaluated and adopted 16S rDNA community profiling protocols for ABI 3730 and 454 FLX Titanium sequencing. In the course of establishing protocols, we examined the performance and error characteristics of each technology, and the relationship of sequence error to the utility of 16S rDNA regions for classification- and OTU-based analysis of community structure. The data production protocols used for this work are those used by the participating centers to produce 16S rDNA sequence for the Human Microbiome Project. Thus, these results can be informative for interpreting the large body of clinical 16S rDNA data produced for this project.     

Microbiome predators in changing soils

Microbiome predators shape the soil microbiome and thereby soil functions. However, this knowledge has been obtained from small-scale observations in fundamental rather than applied settings and has focused on a few species under ambient conditions. Therefore, there are several unaddressed questions on soil microbiome predators: (1) What is the role of microbiome predators in soil functioning? (2) How does global change affect microbiome predators and their functions? (3) How can microbiome predators be applied in agriculture? We show that there is sufficient evidence for the vital role of microbiome predators in soils and stress that global changes impact their functions, something that urgently needs to be addressed to better understand soil functioning as a whole. We are convinced that there is a potential for the application of microbiome predators in agricultural settings, as they may help to sustainably increase plant growth. Therefore, we plea for more applied research on microbiome predators.