Lectura 22 Abril 2015

Bacterial biogeography of the human digestive tract
Jennifer C. Stearns, Michael D. J. Lynch1, Dilani B. Senadheera, Howard C. Tenenbaum, Michael B. Goldberg, Dennis G. Cvitkovitch, Kenneth Croitoru, Gabriel Moreno-Hagelsieb & Josh D. Neufeld

We present bacterial biogeography as sampled from the human gastrointestinal tract of four healthy subjects. This study generated .32 million paired-end sequences of bacterial 16S rRNA genes (V3 region) representing .95,000 unique operational taxonomic units (OTUs; 97% similarity clusters), with .99% Good’s coverage for all samples. The highest OTU richness and phylogenetic diversity was found in the mouth samples. The microbial communities of multiple biopsy sites within the colon were highly similar within individuals and largely distinct from those in stool. Within an individual, OTU overlap among broad site definitions (mouth, stomach/duodenum, colon and stool) ranged from 32–110 OTUs, 25 of which were common to all individuals and included OTUs affiliated with Faecalibacterium prasnitzii and the TM7 phylum. This first comprehensive characterization of the abundant and rare microflora found along the healthy human digestive tract represents essential groundwork to investigate further how the human microbiome relates to health and disease.

Cambio de lectura

Habrá un cambio en las fechas de lecturas intercanbiando de fechas las lecturas del 22 y 29 de Abril, quedando de la siguiente manera:

Miércoles 22 de Abril
Stearns et al. 2011 - Bacterial biogeography of the human digestive tract

Miércoles 29 de Abril
Shade et al. 2014 - Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity.

Lectura 20 Abril 2015

Structure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium

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.

Lectura 15 Abril 2015

The Neolithic revolution of bacterial genomes
Alex Mira, Ravindra Pushker and Francisco Rodríguez-Valera

Current human activities undoubtedly impact natural ecosystems. However, the influence of Homo sapiens on living organisms must have also occurred in the past. Certain genomic characteristics of prokaryotes can be used to study the impact of ancient human activities on microorganisms. By analyzing DNA sequence similarity features of transposable elements, dramatic genomic changes have been identified in bacteria that are associated with large and stable human communities, agriculture and animal domestication: three features unequivocally linked to the Neolithic revolution. It is hypothesized that bacteria specialized in human-associated niches underwent an intense transformation after the social and demographic changes that took place with the first Neolithic settlements. These genomic changes are absent in related species that are not specialized in humans.

Lectura 13 Abril 2015

The Tiniest Tiny Genomes
Nancy A. Moran and Gordon M. Bennett


Starting in 2006, surprisingly tiny genomes have been discovered from numerous bacterial symbionts of insect hosts. Despite their size, each retains some genes that enable provisioning of limiting nutrients or other capabilities required by hosts. Genome sequence analyses show that genome reduction is an ongoing process, resulting in a continuum of sizes, with the smallest genome currently known at 112 kilobases. Genome reduction is typical in host-restricted symbionts and pathogens, but the tiniest genomes are restricted to symbionts required by hosts and restricted to specialized host cells, resulting from long coevolution with hosts. Genes are lost in all functional categories, but core genes for central informational processes, including genes encoding ribosomal proteins, are mostly retained, whereas genes underlying production of cell envelope components are especially depleted. Thus, these entities retain cell-like properties but are heavily dependent on coadaptation of hosts, which continuously evolve to support the symbionts upon which they depend.

Lectura 08 Abril 2015

Defining the core Arabidopsis thaliana root microbiome

Derek S. Lundberg, Sarah L. Lebeis, Sur Herrera Paredes, Scott Yourstone, Jase Gehring, Stephanie Malfatti, Julien Tremblay, Anna Engelbrektson,VictorKunin, Tijana Glavina del Rio, Robert C. Edgar, Thilo Eickhorst, Ruth E. Ley, Philip Hugenholtz, Susannah Green Tringe & Jeffery L. Dangl

Land plants associate with a root microbiota distinct from the complex microbial community present in surrounding soil. The microbiota colonizing the rhizosphere (immediately surroundingthe root) and the endophytic compartment (within the root) contribute to plant growth, productivity, carbon sequestration and phytoremediation. Colonization of the root occurs despite a sophisticated plant immune system, suggesting finely tuned discrimination of mutualists and commensals from pathogens. Genetic principles governing the derivation of host-specific endophyte communities from soil communities are poorly understood. Here we report the pyrosequencing of the bacterial 16S ribosomal RNA gene of more than 600 Arabidopsis thaliana plants to test the hypotheses that the root rhizosphere and endophytic compartmentmicrobiota of plants grown under controlled conditions in natural soils are sufficiently dependent on the host to remain consistent across different soil types and developmental stages, and sufficiently dependent on host genotype to vary between inbred Arabidopsis accessions. We describe different bacterial communities in two geochemically distinct bulk soils and in rhizosphere and endophytic compartments prepared from roots grown in these soils. The communities in each compartment are strongly influenced by soil type. Endophytic compartments fromboth soils feature overlapping, low-complexity communities that are markedly enriched in Actinobacteria and specific families from other phyla, notably Proteobacteria. Some bacteria vary quantitatively between plants of different developmental stage and genotype. Our rigorous definition of an endophytic compartment microbiome should facilitate controlled dissection of plant–microbe interactions derived from complex soil communities.

Lectura 06 Abril 2015

Bacterial-Fungal Interactions: Hyphens between Agricultural, Clinical,Environmental, and Food Microbiologists
P. Frey-Klett, P. Burlinson, A. Deveau, M. Barret, M. Tarkka, and A. Sarniguet