Draft genome sequences of two Pseudomonas strains isolated from 129I plumes at the Hanford Site.

Pseudomonas strains DVZ6 and DVZ24 were isolated from a sediment trap incubated in an 129I plume at the Hanford Site (Washington State, USA). Whole-genome sequencing of the strains revealed that both genomes are 5.77 Mb in size, with a G + C content of 64.75%.

Draft genome sequence of Enterobacter hormaechei DVZ29, an iodide-oxidizing bacterium isolated from the Hanford site.

Enterobacter hormaechei DVZ29 was isolated from a sediment trap incubated in an 129I plume at the Hanford Site (Washington State, USA). A whole genome sequencing of the strain resulted in 32 contigs and revealed that the genome is 4.90 Mb, with a G + C content of 55.61%.

Complete Genome Sequences of Subcluster C1 Mycobacteriophages Blackbrain, Cactojaque, Kboogie, Trinitium, and YoungMoneyMata.

Five subcluster C1 mycobacteriophages, Blackbrain, Cactojaque, Kboogie, Trinitium, and YoungMoneyMata, were isolated from soil using the host Mycobacterium smegmatis mc2155. The genome sizes range from 154,512 to 156,223 bp. The largest genome encodes 237 predicted proteins, 34 tRNAs, and 1 transfer-messenger RNA (tmRNA).

Complete Genome Sequences of Mycobacteriophages SynergyX, Abinghost, Bananafish, and Delton.

Four lytic mycobacteriophages, namely, SynergyX, Abinghost, Bananafish, and Delton, were isolated from soil in Washington, DC, using the bacterial host Mycobacterium smegmatis mc2155. Analysis of the genomes revealed that they belong to two subclusters of actinobacteriophage cluster B (subclusters B2 and B3) and subcluster D1 of cluster D.

Complete Genome Sequences of Mycobacteriophages Dallas and Jonghyun.

Two temperate mycobacteriophages, Dallas and Jonghyun, were isolated from soil in Washington, DC, using the bacterial host Mycobacterium smegmatis mc2155. Analysis of the genomes revealed that Dallas and Jonghyun belong to clusters J and G, respectively. The structures of the genomes are typical of their respective clusters.

Prophage-mediated defence against viral attack and viral counter-defence.

Temperate phages are common, and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses that infect mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere with the infection of lytic and temperate phages that are either closely related (homotypic defence) or unrelated (heterotypic defence) to the prophage. Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defence systems include a single-subunit restriction system, a heterotypic exclusion system and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, which acts as a highly effective counter-defence system. Prophage-mediated viral defence offers an efficient mechanism for bacterial success in host-virus dynamics, and counter-defence promotes phage co-evolution.

Genome Sequence of Mycobacteriophage ErnieJ.

ErnieJ, a cluster C mycobacteriophage that infects Mycobacterium smegmatis mc2155, was recovered from soil in Washington, DC. Its genome is 153,243 bp in size and encodes 227 predicted proteins, 30 tRNAs, and one transfer-messenger RNA (tmRNA). Ten percent of the predicted proteins have homologs in phages that infect nonmycobacterial Actinobacteria.

The effects of intestinal microbial community structure on disease manifestation in IL-10-/- mice infected with Helicobacter hepaticus.

BACKGROUND: The aberrant inflammation that is the hallmark of the inflammatory bowel diseases (IBD) is associated with several factors, including changes in the intestinal microbiota. Here, we confirmed that an intestinal microbiota is needed for development of typhlocolitis in Helicobacter hepaticus infected IL-10-/- C57BL/6 mice, and investigated the role of the microbiota in modulating disease. RESULTS: We altered the murine microbiota by treatment with the antibiotics vancomycin or cefoperazone prior to H. hepaticus infection. Through surveys of the 16S rRNA encoding-gene, analyses of histology and changes in expression of host mediators, we correlated alterations in the microbiota with host responses. We found that resident microbes are essential for initiation of disease, as animals mono-associated with H. hepaticus did not develop colitis. Despite the requirement for an indigenous microbiota for the initiation of disease, the severity of disease was independent of antibiotic-induced changes in the microbial community structure. Despite differences in the expression of host inflammatory mediators associated with shifts in the microbiota, H. hepaticus infection led to similar histopathologic lesions in microbial communities exposed to either cefoperazone or vancomycin. CONCLUSION: In conclusion, we demonstrate that colitis due to H. hepaticus infection can be initiated and progress in the presence of several different microbial communities. Furthermore, H. hepaticus is the main driver of inflammation in this model, while the specific structure of the microbiota may modulate the host pathways that lead to chronic inflammation.

Antibiotic administration alters the community structure of the gastrointestinal micobiota.

We recently demonstrated that antibiotic administration has a reproducible effect on the community structure of the indigenous gastrointestinal microbiota of mice. In this addendum we report on additional experimentation using the antibiotic vancomycin. In accord with our previous findings, vancomycin administration results in consistent alteration of the microbiota of the cecal contents and the cecal mucosa. These alterations are largely reversed by a three-week period of recovery without antibiotics. In contrast to our previous results using other antibiotics, the alterations in community structure associated with vancomycin occured without a significant decrease in the overall bacterial biomass. These results indicate that different antibiotics have specific effects on the gut microbiota. This points the way towards targeted, therapeutic alteration of the gut bacterial community as a whole.

From structure to function: the ecology of host-associated microbial communities.

In the past several years, we have witnessed an increased interest in understanding the structure and function of the indigenous microbiota that inhabits the human body. It is hoped that this will yield novel insight into the role of these complex microbial communities in human health and disease. What is less appreciated is that this recent activity owes a great deal to the pioneering efforts of microbial ecologists who have been studying communities in non-host-associated environments. Interactions between environmental microbiologists and human microbiota researchers have already contributed to advances in our understanding of the human microbiome. We review the work that has led to these recent advances and illustrate some of the possible future directions for continued collaboration between these groups of researchers. We discuss how the application of ecological theory to the human-associated microbiota can lead us past descriptions of community structure and toward an understanding of the functions of the human microbiota. Such an approach may lead to a shift in the prevention and treatment of human diseases that involves conservation or restoration of the normal community structure and function of the host-associated microbiota.

Robustness of the bacterial community in the cabbage white butterfly larval midgut.

Microbial communities typically vary in composition and structure over space and time. Little is known about the inherent characteristics of communities that govern various drivers of these changes, such as random variation, changes in response to perturbation, or susceptibility to invasion. In this study, we use 16S ribosomal RNA gene sequences to describe variation among bacterial communities in the midguts of cabbage white butterfly (Pieris rapae) larvae and examine the influence of community structure on susceptibility to invasion. We compared communities in larvae experiencing the same conditions at different times (temporal variation) or fed different diets (perturbation). The most highly represented phylum was Proteobacteria, which was present in all midgut communities. The observed species richness ranged from six to 15, and the most abundant members affiliated with the genera Methylobacteria, Asaia, Acinetobacter, Enterobacter, and Pantoea. Individual larvae subjected to the same conditions at the same time harbored communities that were highly similar in structure and membership, whereas the communities observed within larval populations changed with diet and over time. In addition, structural changes due to perturbation coincided with enhanced susceptibility to invasion by Enterobacter sp. NAB3R and Pantoea stewartii CWB600, suggesting that resistance to invasion is in part governed by community structure. These findings along with the observed conservation of membership at the phylum level, variation in structure and membership at lower taxonomic levels, and its relative simplicity make the cabbage white butterfly larval community an attractive model for studying community dynamics and robustness.

Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities.

mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the alpha and beta diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.

Contributions of gut bacteria to Bacillus thuringiensis-induced mortality vary across a range of Lepidoptera.

BACKGROUND: Gut microbiota contribute to the health of their hosts, and alterations in the composition of this microbiota can lead to disease. Previously, we demonstrated that indigenous gut bacteria were required for the insecticidal toxin of Bacillus thuringiensis to kill the gypsy moth, Lymantria dispar. B. thuringiensis and its associated insecticidal toxins are commonly used for the control of lepidopteran pests. A variety of factors associated with the insect host, B. thuringiensis strain, and environment affect the wide range of susceptibilities among Lepidoptera, but the interaction of gut bacteria with these factors is not understood. To assess the contribution of gut bacteria to B. thuringiensis susceptibility across a range of Lepidoptera we examined larval mortality of six species in the presence and absence of their indigenous gut bacteria. We then assessed the effect of feeding an enteric bacterium isolated from L. dispar on larval mortality following ingestion of B. thuringiensis toxin. RESULTS: Oral administration of antibiotics reduced larval mortality due to B. thuringiensis in five of six species tested. These included Vanessa cardui (L.), Manduca sexta (L.), Pieris rapae (L.) and Heliothis virescens (F.) treated with a formulation composed of B. thuringiensis cells and toxins (DiPel), and Lymantria dispar (L.) treated with a cell-free formulation of B. thuringiensis toxin (MVPII). Antibiotics eliminated populations of gut bacteria below detectable levels in each of the insects, with the exception of H. virescens, which did not have detectable gut bacteria prior to treatment. Oral administration of the Gram-negative Enterobacter sp. NAB3, an indigenous gut resident of L. dispar, restored larval mortality in all four of the species in which antibiotics both reduced susceptibility to B. thuringiensis and eliminated gut bacteria, but not in H. virescens. In contrast, ingestion of B. thuringiensis toxin (MVPII) following antibiotic treatment significantly increased mortality of Pectinophora gossypiella (Saunders), which was also the only species with detectable gut bacteria that lacked a Gram-negative component. Further, mortality of P. gossypiella larvae reared on diet amended with B. thuringiensis toxin and Enterobacter sp. NAB3 was generally faster than with B. thuringiensis toxin alone. CONCLUSION: This study demonstrates that in some larval species, indigenous gut bacteria contribute to B. thuringiensis susceptibility. Moreover, the contribution of enteric bacteria to host mortality suggests that perturbations caused by toxin feeding induce otherwise benign gut bacteria to exert pathogenic effects. The interaction between B. thuringiensis and the gut microbiota of Lepidoptera may provide a useful model with which to identify the factors involved in such transitions.

Quorum-sensing signals in the microbial community of the cabbage white butterfly larval midgut.

The overall goal of this study was to examine the role of quorum-sensing (QS) signals in a multispecies microbial community. Toward this aim, we studied QS signals produced by an indigenous member and an invading pathogen of the microbial community of the cabbage white butterfly (CWB) larval midgut (Pieris rapae). As an initial step, we characterized the QS system in Pantoea CWB304, which was isolated from the larval midgut. A luxI homolog, designated panI, is necessary for the production of N-acyl-L-homoserine lactones (AHLs) by Pantoea CWB304. To determine whether AHL signals are exchanged in the alkaline environment of the midgut, we constructed AHL-sensing bioluminescent reporter strains in Pantoea CWB304 and a panI mutant of this strain. In the gut of the CWB larvae, the reporter in an AHL-deficient Pantoea CWB304 detected AHLs when coinoculated with the wild type. To study the role of AHL signals produced by a community invader, we examined pathogenesis of Pseudomonas aeruginosa PAO1 in CWB larvae. Mortality induced by P. aeruginosa PAO1 was significantly reduced when signaling was interrupted by either a potent chemical inhibitor of QS or mutations in the lasI and rhlI AHL synthases of P. aeruginosa PAO1. These results show that AHLs are exchanged among bacteria in the alkaline gut of CWB larvae and contribute to disease caused by P. aeruginosa PAO1.

Rules of engagement: interspecies interactions that regulate microbial communities.

Microbial communities comprise an interwoven matrix of biological diversity modified by physical and chemical variation over space and time. Although these communities are the major drivers of biosphere processes, relatively little is known about their structure and function, and predictive modeling is limited by a dearth of comprehensive ecological principles that describe microbial community processes. Here we discuss working definitions of central ecological terms that have been used in various fashions in microbial ecology, provide a framework by focusing on different types of interactions within communities, review the status of the interface between evolutionary and ecological study, and highlight important similarities and differences between macro- and microbial ecology. We describe current approaches to study microbial ecology and progress toward predictive modeling.