Genome sequence of , isolated from a red-backed salamander () in Rugar Woods, NY, USA.

Here we present the complete genome sequence of isolated from a red-backed salamander in Rugar Woods, Plattsburgh, NY, USA. The assembled genome comprises a 4.3 Mb chromosome with a guanine-cytosine content of 33.

Draft genome sequence of sp. ABKF26, a potential petroleum, plastic, and rubber-degrading bacterium, isolated from St. Albans Bay, VT, USA.

Here, we present the draft genome sequence of sp. ABKF26, a potential petroleum, plastic, and rubber degrading bacterium isolated from Lake Champlain. The assembled genome comprises a 6.

Genome sequence of RI06-95 isolated during a bloom in lake Champlain, USA.

Here, we present the complete genome sequence of RI06-95 isolated during a bloom in Lake Champlain. The assembled genome comprises a 3.8 Mbp chromosome with a GC content of 42%, and two plasmids, pPZZ84 6.

Enhancing Microbiome Research through Genome-Scale Metabolic Modeling.

Construction and analysis of genome-scale metabolic models (GEMs) is a well-established systems biology approach that can be used to predict metabolic and growth phenotypes. The ability of GEMs to produce mechanistic insight into microbial ecological processes makes them appealing tools that can open a range of exciting opportunities in microbiome research. Here, we briefly outline these opportunities, present current rate-limiting challenges for the trustworthy application of GEMs to microbiome research, and suggest approaches for moving the field forward.

Predicted Metabolic Function of the Gut Microbiota of Drosophila melanogaster.

An important goal for many nutrition-based microbiome studies is to identify the metabolic function of microbes in complex microbial communities and their impact on host physiology. This research can be confounded by poorly understood effects of community composition and host diet on the metabolic traits of individual taxa. Here, we investigated these multiway interactions by constructing and analyzing metabolic models comprising every combination of five bacterial members of the gut microbiome (from single taxa to the five-member community of and species) under three nutrient regimes.

Impact of Facultative Bacteria on the Metabolic Function of an Obligate Insect-Bacterial Symbiosis.

Beneficial microorganisms associated with animals derive their nutritional requirements entirely from the animal host, but the impact of these microorganisms on host metabolism is largely unknown. The focus of this study was the experimentally tractable tripartite symbiosis between the pea aphid , its obligate intracellular bacterial symbiont , and the facultative bacterium which is localized primarily to the aphid hemolymph (blood). Metabolome experiments on, first, multiple aphid genotypes that naturally bear or lack and, second, one aphid genotype from which was experimentally eliminated revealed no significant effects of on aphid metabolite profiles, indicating that does not cause major reconfiguration of host metabolism.

Syntrophic splitting of central carbon metabolism in host cells bearing functionally different symbiotic bacteria.

Insects feeding on the nutrient-poor diet of xylem plant sap generally bear two microbial symbionts that are localized to different organs (bacteriomes) and provide complementary sets of essential amino acids (EAAs). Here, we investigate the metabolic basis for the apparent paradox that xylem-feeding insects are under intense selection for metabolic efficiency but incur the cost of maintaining two symbionts for functions mediated by one symbiont in other associations. Using stable isotope analysis of central carbon metabolism and metabolic modeling, we provide evidence that the bacteriomes of the spittlebug Clastoptera proteus display high rates of aerobic glycolysis, with syntrophic splitting of glucose oxidation.

Genetically similar temperate phages form coalitions with their shared host that lead to niche-specific fitness effects.

Temperate phages engage in long-term associations with their hosts that may lead to mutually beneficial interactions, of which the full extent is presently unknown. Here, we describe an environmentally relevant model system with a single host, a species of the Roseobacter clade of marine bacteria, and two genetically similar phages (ɸ-A and ɸ-D). Superinfection of a ɸ-D lysogenized strain (CB-D) with ɸ-A particles resulted in a lytic infection, prophage induction, and conversion of a subset of the host population, leading to isolation of a newly ɸ-A lysogenized strain (CB-A).

The Metabolome of Associations between Xylem-Feeding Insects and their Bacterial Symbionts.

Metabolomics has increasingly led to important insights in chemical ecology by identifying environmentally relevant small molecules that mediate inter-organismal interactions. Nevertheless, the application of metabolomics to investigate interactions between phytophagous insects and their microbial symbionts remains underutilized. Here, we investigated the metabolomes of the bacteriomes (organs bearing symbiotic bacteria) isolated from natural populations of five species of xylem-feeding insects.

The Cost of Metabolic Interactions in Symbioses between Insects and Bacteria with Reduced Genomes.

Various intracellular bacterial symbionts that provide their host with essential nutrients have much-reduced genomes, attributed largely to genomic decay and relaxed selection. To obtain quantitative estimates of the metabolic function of these bacteria, we reconstructed genome- and transcriptome-informed metabolic models of three xylem-feeding insects that bear two bacterial symbionts with complementary metabolic functions: a primary symbiont, , that has codiversified with the insects, and a coprimary symbiont of distinct taxonomic origin and with different degrees of genome reduction in each insect species ( in a cicada, in a sharpshooter, and in a spittlebug). Our simulations reveal extensive bidirectional flux of multiple metabolites between each symbiont and the host, but near-complete metabolic segregation (i.

Nutrient factories: metabolic function of beneficial microorganisms associated with insects.

Many symbiotic microorganisms in animals, including insects, have parallels to microbial nutrient factories of biotechnology: just as the metabolism of individual microorganisms and microbial communities is modified by biotechnologists to produce specific nutrients, so the many insect-associated microorganisms synthesize specific nutrients that support the sustained growth and reproduction of their animal host. Three broad metabolic functions are mediated by insect-associated microorganisms: (i) fermentation of dietary constituents, releasing products that contribute to host carbon and energy metabolism; (ii) overproduction of nutrients, notably essential amino acids, required by the host and (iii) recycling of host waste metabolites. In many systems, the nutrients that are released from living microbial cells have been identified, with evidence for metabolite cross-feeding and shared metabolic pathways both among different microbial taxa and between microorganisms and the host.

Cooperative Metabolism in a Three-Partner Insect-Bacterial Symbiosis Revealed by Metabolic Modeling.

An important factor determining the impact of microbial symbionts on their animal hosts is the balance between the cost of nutrients consumed by the symbionts and the benefit of nutrients released back to the host, but the quantitative significance of nutrient exchange in symbioses involving multiple microbial partners has rarely been addressed. In this study on the association between two intracellular bacterial symbionts, " Portiera aleyrodidarum" and " Hamiltonella defensa," and their animal host, the whitefly , we apply metabolic modeling to investigate host-symbiont nutrient exchange. Our analysis revealed that >60% of the essential amino acids and related metabolites synthesized by " Portiera aleyrodidarum" are utilized by the host, including a substantial contribution of nitrogen recycled from host nitrogenous waste, and that these interactions are required for host growth.

Draft Genome Sequence of Sulfitobacter sp. CB2047, a Member of the Roseobacter Clade of Marine Bacteria, Isolated from an Emiliania huxleyi Bloom.

We announce the draft genome sequence of Sulfitobacter sp. strain CB2047, a marine bacterium of the Roseobacter clade, isolated from a phytoplankton bloom. The genome encodes pathways for the catabolism of aromatic compounds as well as transformations of carbon monoxide and sulfur species.

Genome Sequences of Two Temperate Phages, ΦCB2047-A and ΦCB2047-C, Infecting Sulfitobacter sp. Strain 2047.

We announce the complete genome sequences of two temperate Podoviridae, Sulfitobacter phages ΦCB2047-A and ΦCB2047-C, which infect Sulfitobacter sp. strain 2047, a member of the Roseobacter clade. This is the first report of temperate podophage infecting members of the Sulfitobacter genus of the Roseobacter clade.

Genome Sequence of the Sulfitobacter sp. Strain 2047-Infecting Lytic Phage {Phi}CB2047-B.

We announce the complete genome sequence of a lytic podovirus, ΦCB2047-B, which infects the bacterium Sulfitobacter sp. strain 2047, a member of the Roseobacter clade. Genome analysis revealed ΦCB2047-B to be an N4-like phage, with its genome having high nucleotide similarity to other N4-like roseophage genomes.

Phage infection of an environmentally relevant marine bacterium alters host metabolism and lysate composition.

Viruses contribute to the mortality of marine microbes, consequentially altering biological species composition and system biogeochemistry. Although it is well established that host cells provide metabolic resources for virus replication, the extent to which infection reshapes host metabolism at a global level and the effect of this alteration on the cellular material released following viral lysis is less understood. To address this knowledge gap, the growth dynamics, metabolism and extracellular lysate of roseophage-infected Sulfitobacter sp.