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The human microbiome is the sum of all microbiota, their genes, and their mobile genetic elements associated with an individual. These microbiota, which include bacteria, archaea, fungi, micro-eukaryotes and viruses, form complex ecological communities across the human body, including the gastrointestinal tract and skin. Ancient humans carried their microbiomes as they dispersed across the globe, and some contemporary microbiota are known to have colonized humans prior to out of Africa migrations. Yet how microbiomes co-evolved with their hosts, and how present-day microbiomes relate to patterns of human migration remains largely to be explored. Aside from a few exceptions, including dental calculus and coprolite samples, ancient microbiomes cannot be studied directly in the same manner as skeletal or archaeological artifacts, because they are not well pre- served in human remains. However, genomic and metagenomic studies of pre- sent day microbiomes across ethnicities and geography may allow inference of human evolution and dispersal. Doing so requires microbiome data from across the globe, but so far human microbiome research has mostly characterized popu- lations from Europe, North America, and Asia. Much of the African microbiome remains largely under-sampled, limiting inference for questions of co-evolution and human dispersal. African populations harbor vast genomic and cultural diver- sity, with some populations still relatively isolated from the microbially-disruptive aspects of modern lifestyles (e.g., antibiotics, antimicrobial soap). This chapter reviews our current understanding of the factors which shape the gut micro- biome of living African populations, both industrialized and pre-industrialized, and reviews efforts to use human-associated microbes as tracers of early human migrations.

The applicability of next generation DNA sequencing (NGS) methods for water quality assessment has so far not been broadly investigated. This study set out to evaluate the potential of an NGS-based approach in a complex catchment with importance for drinking water abstraction. In this multicompartment investigation, total bacterial communities in water, faeces, soil, and sediment samples were investigated by 454 pyrosequencing of bacterial 16S rRNA gene amplicons to assess the capabilities of this NGS method for (i) the development and evaluation of environmental molecular diagnostics, (ii) direct screening of the bulk bacterial communities, and (iii) the detection of faecal pollution in water. Results indicate that NGS methods can highlight potential target populations for diagnostics and will prove useful for the evaluation of existing and the development of novel DNA-based detection methods in the field of water microbiology. The used approach allowed unveiling of dominant bacterial populations but failed to detect populations with low abundances such as faecal indicators in surface waters. In combination with metadata, NGS data will also allow the identification of drivers of bacterial community composition during water treatment and distribution, highlighting the power of this approach for monitoring of bacterial regrowth and contamination in technical systems.

The rhizosphere is a critical interface supporting the exchange of resources between plants and their associated soil environment. Rhizosphere microbial diversity is influenced by the physical and chemical properties of the rhizosphere, some of which are determined by the genetics of the host plant. However, within a plant species, the impact of genetic variation on the composition of the microbiota is poorly understood. Here, we characterized the rhizosphere bacterial diversity of 27 modern maize inbreds possessing exceptional genetic diversity grown under field conditions. Randomized and replicated plots of the inbreds were planted in five field environments in three states, each with unique soils and management conditions. Using pyrosequencing of bacterial 16S rRNA genes, we observed substantial variation in bacterial richness, diversity, and relative abundances of taxa between bulk soil and the maize rhizosphere, as well as between fields. The rhizospheres from maize inbreds exhibited both a small but significant proportion of heritable variation in total bacterial diversity across fields, and substantially more heritable variation between replicates of the inbreds within each field. The results of this study should facilitate expanded studies to identify robust heritable plant–microbe interactions at the level of individual polymorphisms by genome wide association, so that plant-microbiome interactions can ultimately be incorporated into plant breeding.

Our adult bodies harbor ~10 times more microbial than human cells. Their genomes (the microbiome) endow us with physiologic capacities that we have not had to evolve on our own and thus are both a manifestation of who we are genetically and metabolically, and a reflection of our state of well-being. Our distal gut is the highest density natural bacterial ecosystem known, the most comprehensively surveyed to date, and the most highly represented in pure culture. It contains more bacterial cells than all of our other microbial communities combined. To obtain a more comprehensive view of our biol-ogy, we propose a human gut microbiome initiative (HGMI) that will deliver deep draft whole genome sequences for 100 species representing the bacterial divisions (superkingdoms) known to comprise our distal gut microbiota: 15 of these genomes will be selected for finishing. A cost-effective strategy in-volves producing the bulk of the coverage by shotgun reads on a 454 Life Sciences pyrosequencer. Long-range linking information will be provided by paired end reads of fosmid subclones using a con-ventional ABI 3730xl capillary machine. The bulk of our sequencing will use human-derived strains, representing targeted phylotypes, from existing culture collections. The list will be augmented by in vivo culture of a human fecal microbiota in gnotobiotic mice. The latter approach will be used to obtain vastly simplified consortia, or pure cultures of previously uncultured representatives of important gut-associated bacteria. The deposited curated genome sequences will herald another phase of completion of the 'human' genome sequencing project, provide a key reference for metagenome projects, and serve as a model for future initiatives that seek to characterize our other extra-intestinal microbial communities.

In this report we present the latest experimental results on electron beam neutralization. These experiments have been made at LEAR and on the JINR test bench. The main difficulty in obtaining neutralized beams resides in an instability which is dependent on the electron beam current. A number of methods have been developed in order to overcome this instability and have enabled us to further investigate the possibility of generating intense low energy electron beams for the cooling of Pb ions.