To assess the bacterial diversity of marine sediments, a culture-dependent approach was employed to assess the diversity of Gram-positive bacteria in marine sediments collected around the islands of Palau. The survey of the total, aerobic Gram-positive bacterial diversity present in tropical marine sediments resulted in the isolation of a diverse assemblage of Gram-positive isolates. Of the 78 operational taxonomic units cultured (OTUs based on = 98% 16S rRNA gene sequence identity), 52 were determined to be members of the order Actinomycetales and 26 were determined to be members of the order Bacillales. Bacterial genome sequencing has provided opportunities to assess the secondary metabolite biosynthetic potential of individual strains. By elucidating entire biosynthetic pathways in the context of all other genes and pathways present, it is also possible to address questions related to the evolution of gene clusters or individual genes within a cluster. The complete genome sequence of Salinispora arenicola strain CNS-205, an actinomycete isolated during the research expedition to Palau, provided an opportunity to investigate the evolution of type I modular polyketide synthase (PKS) gene clusters. While a tremendous amount can be learned from analyzing the entire genetic blueprint of a microorganism, additional natural product discovery approaches are necessary to gain insight into the biosynthetic potential of unsequenced organisms prior to fermentation, extraction and chemical analyses. A PCR based approach has been used successfully to suggest which representative isolates from the 52 Actinomycetales OTUs harbor type I PKS, enediyne PKS and nonribosomal peptide synthetase (NRPS) pathways. Over half of the cultured Actinomycetales OTUs were found to possess genes associated with at least one PKS or NRPS biosynthetic pathway and although some of these actinomycetes represent families well known to produce secondary metabolites, the results suggest that novel secondary metabolites can be isolated from both filamentous and unicellular actinomycete families. In addition to determining if these pathways are present, a phylogenetic approach was used successfully to suggest the number and novelty of type I PKS pathways present. By using the phylogenetic approach, the diversity, novelty and identity of type I PKS metabolites can be predicted

Actinomycetes were cultivated using a variety of media and selective isolation techniques from 275 marine samples collected around the island of Guam. In total, 6425 actinomycete colonies were observed and 983 (15%) of these, representing the range of morphological diversity observed from each sample, were obtained in pure culture. The majority of the strains isolated (58%) required seawater for growth indicating a high degree of marine adaptation. The dominant actinomycete recovered (568 strains) belonged to the seawater-requiring marine taxon 'Salinospora', a new genus within the family Micromonosporaceae. A formal description of this taxon has been accepted for publication (Maldonado et al., 2005) and includes a revision of the generic epithet to Salinispora gen. nov. Members of two major new clades related to Streptomyces spp., tentatively called MAR2 and MAR3, were cultivated and appear to represent new genera within the Streptomycetaceae. In total, five new marine phylotypes, including two within the Thermomonosporaceae that appear to represent new taxa, were obtained in culture. These results support the existence of taxonomically diverse populations of phylogenetically distinct actinomycetes residing in the marine environment. These bacteria can be readily cultured using low nutrient media and represent an unexplored resource for pharmaceutical drug discovery.

Genomic islands have been shown to harbor functional traits that differentiate ecologically distinct populations of environmental bacteria. A comparative analysis of the complete genome sequences of the marine Actinobacteria Salinispora tropica and Salinispora arenicola reveals that 75% of the species-specific genes are located in 21 genomic islands. These islands are enriched in genes associated with secondary metabolite biosynthesis providing evidence that secondary metabolism is linked to functional adaptation. Secondary metabolism accounts for 8.8% and 10.9% of the genes in the S. tropica and S. arenicola genomes, respectively, and represents the major functional category of annotated genes that differentiates the two species. Genomic islands harbor all 25 of the species-specific biosynthetic pathways, the majority of which occur in S. arenicola and may contribute to the cosmopolitan distribution of this species. Genome evolution is dominated by gene duplication and acquisition, which in the case of secondary metabolism provide immediate opportunities for the production of new bioactive products. Evidence that secondary metabolic pathways are exchanged horizontally, coupled with earlier evidence for fixation among globally distributed populations, supports a functional role and suggests that the acquisition of natural product biosynthetic gene clusters represents a previously unrecognized force driving bacterial diversification. Species-specific differences observed in clustered regularly interspaced short palindromic repeat sequences suggest that S. arenicola may possess a higher level of phage immunity, whereas a highly duplicated family of polymorphic membrane proteins provides evidence for a new mechanism of marine adaptation in Gram-positive bacteria.

Investigations of gut microbiomes have shed light on the diversity and genetic content of these communities, and helped shape our understanding of how host-associated microorganisms influence host physiology, behavior, and health. Despite the importance of gut microbes to metazoans, our understanding of the changes in diversity and composition across the alimentary tract, and the source of the resident community are limited. Here, using community metagenomics and 16S rRNA gene sequencing, we assess microbial community diversity and coding potential in the foregut, midgut, and hindgut of a juvenile Panchlora cockroach, which resides in the refuse piles of the leaf-cutter ant species Atta colombica. We found a significant shift in the microbial community structure and coding potential throughout the three gut sections of Panchlora sp., and through comparison with previously generated metagenomes of the cockroach's food source and niche, we reveal that this shift in microbial community composition is influenced by the ecosystems in which Panchlora sp. occurs. While the foregut is composed of microbes that likely originate from the symbiotic fungus gardens of the ants, the midgut and hindgut are composed of a microbial community that is likely cockroach-specific. Analogous to mammalian systems, the midgut and hindgut appear to be dominated by Firmicutes and Bacteroidetes with the capacity for polysaccharide degradation, suggesting they may assist in the degradation of dietary plant material. Our work underscores the prominence of community changes throughout gut microbiomes and highlights ecological factors that underpin the structure and function of the symbiotic microbial communities of metazoans.