Steps in Metagenomics: Let’s Avoid Garbage in and Garbage Out

Is metagenomics a revolution or a new fad? Metagenomics is tightly associated with the availability of next-generation sequencing in all its implementations. The key feature of these new technologies, moving beyond the Sanger-based DNA sequencing approach, is the depth of nucleotide sequencing per sample.1 Knowing much more about a sample changes the traditional paradigms of “What is the most abundant?” or “What is the most significant?” to “What is present and potentially sig­nificant that might influence the situation and outcome?” Let’s take the case of identifying proper biomarkers of disease state in the context of chronic disease prevention. Prevention has been deemed as a viable option to avert human chronic diseases and to curb health­care management costs.2 The actual implementation of any effective preventive measures has proven to be rather difficult. In addition to the typically poor compliance of the general public, the vagueness of the successful validation of habit modification on the long-term risk, points to the need of defining new biomarkers of disease state. Scientists and the public are accepting the fact that humans are super-organisms, harboring both a human genome and a microbial genome, the latter being much bigger in size and diversity, and key for the health of individuals.3,4 It is time to investigate the intricate relationship between humans and their associated microbiota and how this relationship mod­ulates or affects both partners.5 These remarks can be expanded to the animal and plant kingdoms, and holistically to the Earth’s biome. By its nature, the evolution and function of all the Earth’s biomes are influenced by a myriad of interactions between and among microbes (planktonic, in biofilms or host associated) and the surrounding physical environment. The general definition of metagenomics is the cultivation-indepen­dent analysis of the genetic information of the collective genomes of the microbes within a given environment based on its sampling. It focuses on the collection of genetic information through sequencing that can target DNA, RNA, or both. The subsequent analyses can be solely fo­cused on sequence conservation, phylogenetic, phylogenomic, function, or genetic diversity representation including yet-to-be annotated genes. The diversity of hypotheses, questions, and goals to be accomplished is endless. The primary design is based on the nature of the material to be analyzed and its primary function

Influence of structure on the optical limiting properties of nanotubes

We investigate the role of carbon nanotubes structure on their optical limiting properties. Samples of different and well-characterized structural features are studied by optical limiting and pump-probe experiments. The influence of the diameter's size on the nano-object is demonstrated. Indeed, both nucleation and growth of gas bubbles are expected to be sensitive to diameter

Structure, function and diversity of the healthy human microbiome

Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome

Metagenomics for Bacteriology

The study of bacteria, or bacteriology, has gone through transformative waves since its inception in the 1600s. It all started by the visualization of bacteria using light microscopy by Antonie van Leeuwenhoek, when he first described “animalcules.” Direct cellular observation then evolved into utilizing different wavelengths on novel platforms such as electron, fluorescence, and even near-infrared microscopy. Understanding the link between microbes and disease (pathogenicity) began with the ability to isolate and cultivate organisms through aseptic methodologies starting in the 1700s. These techniques became more prevalent in the following centuries with the work of famous scientists such as Louis Pasteur and Robert Koch, and many others since then. The relationship between bacteria and the host’s immune system was first inferred in the 1800s, and to date is continuing to unveil its mysteries. During the last century, researchers initiated the era of molecular genetics. The discovery of the first-generation sequencing technology, the Sanger method, and, later, the polymerase chain reaction technology propelled the molecular genetics field by exponentially expanding the knowledge of relationship between gene structure and function. The rise of commercially available next-generation sequencing methodologies, in the beginning of this century, is drastically allowing larger amount of information to be acquired, in a manner open to the democratization of the approach

Microbiota, Oral Microbiome, and Pancreatic Cancer

Only 30% of patients diagnosed with pancreatic cancer survive one year post-diagnosis. Progress in understanding the causes of pancreatic cancer has been made, including solidifying the associations with obesity and diabetes, and a proportion of cases should be preventable through lifestyle modifications. Unfortunately, identifying reliable biomarkers of early pancreatic cancer has been extremely challenging, and no effective screening modality is currently available for this devastating form of cancer. Recent data suggest the microbiota may play a role in the disease process, but many questions remain. Future studies focusing on the human microbiome, both etiologically and as a marker of disease susceptibility, should shed light on how to better tackle prevention, early detection, and treatment of this highly fatal disease

Promises and Prospects of Microbiome Studies

Since Anthony van Leeuwenhoek, first microscopic observations of the unseen microbiota and the more recent realization that little of the microbes in the biosphere are known, humans have developed a deep curiosity to fully understand the inner workings of the microbial realm. Our ability to characterize the complexity of microbial communities in their natural habitats has dramatically improved over the past decade thanks to advances in high-throughput methodologies. By eliminating the need to isolate and culture individual species, metagenomics approaches have removed many of the obstacles that hindered research in the ecology of mixed microbial consortia, providing valuable information about the diversity, composition, function, and metabolic capability of the community. Microbes are the unseen majority with the capability to colonize every environment, including our bodies. The establishment and composition of a stable human microbiome is determined by the host genetics, immunocompetence, and life-style choices. Our life-style choices determine our exposure to many external and internal environmental factors that permanently or temporarily can influence our microbiome composition. Figure 1 illustrates some of the life-style-related factors that might influence the microbiota of the skin, mouth, and gut. It is not limited to what we carry, touch, breath, and eat. Other dispersal vectors include secretion, excretions, aerosols, air flow, animals, moving surfaces, water, beverages, food, contact, wind, tools, toiletry, and others. These influence the microbiome membership, who are present, and they have the ability to participate in the microbiome dynamic within an environment. The establishment of a microbial community is dependent on many environmental factors, including pH, temperature, altitude, weather, soil type, nutrient availability, relative humidity, air quality, pollutants, microbial competitors, and others. In other words, we are superorganisms interconnected with other living forms on this Earth

A framework for human microbiome research

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies

Resolved simulations of submarine avalanches with a simple soft-sphere / immersed boundary method

Physical mechanisms at the origin of the transport of solid particles in a fluid are still a matter of debate in the physics community. Yet, it is well known that these processes play a fundamental role in many natural configurations, such submarines landslides and avalanches, which may have a significant environmental and economic impact. The goal here is to reproduce the local dynamics of such systems from the grain scale to that of thousands of grains approximately. To this end a simple soft-sphere collision / immersed-boundary method has been developed in order to accurately reproduce the dynamics of a dense granular media collapsing in a viscous fluid. The fluid solver is a finite-volume method solving the three-dimensional, time-dependent Navier-Stokes equations for a incompressible flow on a staggered. Here we use a simple immersed-boundary method consisting of a direct forcing without using any Lagrangian marking of the boundary, the immersed boundary being defined by the variation of a solid volume fraction from zero to one. The granular media is modeled with a discrete element method (DEM) based on a multi-contact soft-sphere approach. In this method, an overlap is allowed between spheres which mimics the elasto-plastic deformation of real grain, and is used to calculate the contact forces based on a linear spring model and a Coulomb criterion. Binary wall-particle collisions in a fluid are simulated for a wide range of Stokes number ranging from 10-¹ to 10⁴. It is shown that good agreement is observed with available experimental results for the whole range of investigated parameters, provided that a local lubrication model is used when the distance of the gap between the particles is below a fraction of the particle radius. A new model predicting the coefficient of restitution as a function of the Stokes number and the relative surface roughness of the particles is proposed. This model, which makes use of no adjustable constant, is shown to be in good agreement with available experimental data. Finally, simulations of dense granular flows in a viscous fluid are performed. The present results are encouraging and open the way for a parametric study in the parameter space initial aspect ratio - initial packing

Multi-spectroscopic investigation of the structure of single-wall carbon nanotubes

We present a multispectroscopic structural study of various nanotube samples with different tube diameters. We determine for each sample the mean bundle and tube diameter as well as the tube diameter distribution. The possibility to work on SWNT of various structural characteristics opens new opportunities to correlate the nanotube structure and their physical properties.Comment: Conf\'{e}rence : 8 au 15 mars 200

Nanotube-based systems for broadband optical limiting: towards an operational system

Nanotube-based systems are good candidates for optical limiting against broadband laser pulses. We explore new routes to improve their limiting performances. We show that the diameter of the nanotubes is a key factor to control the performances. On the other hand, we demonstrate that chemically modified nanotubes can be mixed with organic chromophores, leading to high performance composite limiting systems which are particularly efficient in the nanosecond regime due to the cumulative effects of nonlinear scattering and multiphoton absorption