Recovering complete and draft population genomes from metagenome datasets.

Assembly of metagenomic sequence data into microbial genomes is of fundamental value to improving our understanding of microbial ecology and metabolism by elucidating the functional potential of hard-to-culture microorganisms. Here, we provide a synthesis of available methods to bin metagenomic contigs into species-level groups and highlight how genetic diversity, sequencing depth, and coverage influence binning success. Despite the computational cost on application to deeply sequenced complex metagenomes (e.g., soil), covarying patterns of contig coverage across multiple datasets significantly improves the binning process. We also discuss and compare current genome validation methods and reveal how these methods tackle the problem of chimeric genome bins i.e., sequences from multiple species. Finally, we explore how population genome assembly can be used to uncover biogeographic trends and to characterize the effect of in situ functional constraints on the genome-wide evolution

Correction for Gonzalez et al., "Migraines Are Correlated with Higher Levels of Nitrate-, Nitrite-, and Nitric Oxide-Reducing Oral Microbes in the American Gut Project Cohort".

[This corrects the article DOI: 10.1128/mSystems.00105-16.]

Ecologically Aware Design of Waterway-Encapsulating Structures

Aquatic organism passage (AOP) in waterways-encapsulating structures, particularly culverts, is of growing concern to environmental regulatory agencies, and the Indiana Department of Transportation (INDOT) is seeking systematic responses to this concern in the hydraulic design of such structures. This study reviews design approaches to enhance or accommodate aquatic organism passage through culverts, and proposes a simplified design procedure that requires less data input and analysis, and yet results in a structure complying with the current regional general permit (RGP) conditions. It also makes as much use of already existing INDOT standard specifications for riprap and coarse aggregates that would be as backfill material to form a stable bed within the culvert. The simplified procedure is intended for new larger structures for which a culvert bed needs to be installed, and for expected Indiana conditions of low-gradient ( Because of their larger size compared to traditional culverts, AOP-designed structures are associated with higher installation and material costs, which may however be compensated partially or wholly by lower costs over their operational lifetime. Previous work on life-cycle cost (including social/ecological costs) analysis of AOP-designed culverts was reviewed, but it is concluded that reliable data and methodologies for an adequate analysis are not yet available. The study then explores the consequences of alternative regulatory schemes formulated on the basis of habitat or biotic integrity indices. These may permit simple yet more flexible schemes with the same or even better ecological outcomes

Migraines Are Correlated with Higher Levels of Nitrate-, Nitrite-, and Nitric Oxide-Reducing Oral Microbes in the American Gut Project Cohort.

Nitrates, such as cardiac therapeutics and food additives, are common headache triggers, with nitric oxide playing an important role. Facultative anaerobic bacteria in the oral cavity may contribute migraine-triggering levels of nitric oxide through the salivary nitrate-nitrite-nitric oxide pathway. Using high-throughput sequencing technologies, we detected observable and significantly higher abundances of nitrate, nitrite, and nitric oxide reductase genes in migraineurs versus nonmigraineurs in samples collected from the oral cavity and a slight but significant difference in fecal samples. IMPORTANCE Recent work has demonstrated a potentially symbiotic relationship between oral commensal bacteria and humans through the salivary nitrate-nitrite-nitric oxide pathway (C. Duncan et al., Nat Med 1:546-551, 1995, http://dx.doi.org/10.1038/nm0695-546). Oral nitrate-reducing bacteria contribute physiologically relevant levels of nitrite and nitric oxide to the human host that may have positive downstream effects on cardiovascular health (V. Kapil et al., Free Radic Biol Med 55:93-100, 2013, http://dx.doi.org/10.1016/j.freeradbiomed.2012.11.013). In the work presented here, we used 16S rRNA Illumina sequencing to determine whether a connection exists between oral nitrate-reducing bacteria, nitrates for cardiovascular disease, and migraines, which are a common side effect of nitrate medications (U. Thadani and T. Rodgers, Expert Opin Drug Saf 5:667-674, 2006, http://dx.doi.org/10.1517/14740338.5.5.667)

Reflection and Transmission of Plane Waves at an Interface between Elastic and Micropolar Piezoelectric Solid Half-Spaces

A problem of reflection and transmission of elastic waves at an interface between an elastic solid half-space and a micropolar piezoelectric solid half-space is considered. Both the half-spaces are assumed to be transversely isotropic. For an incident wave from transversely isotropic elastic solid half-space, two reflected waves in transversely isotropic elastic half-space and three transmitted waves in transversely isotropic micropolar piezoelectric solid half-space exist. The appropriate potentials of incident, reflected and transmitted waves satisfy the required boundary conditions at interface and relations in amplitude ratios of all reflected and transmitted waves are obtained with a suitable Snell’s law. The expressions for energy ratios of various reflected and transmitted waves are also obtained. The amplitude ratios and the square root of energy ratios of reflected and transmitted waves are computed numerically for a particular material representing the present model. The amplitude ratios and the square root of energy ratios are plotted against the angle of incidence to observe the effect of micropolar piezoelectricity

Reconstructing an ancestral genotype of two hexachlorocyclohexane-degrading Sphingobium species using metagenomic sequence data.

Over the last 60 years, the use of hexachlorocyclohexane (HCH) as a pesticide has resulted in the production of >4 million tons of HCH waste, which has been dumped in open sinks across the globe. Here, the combination of the genomes of two genetic subspecies (Sphingobium japonicum UT26 and Sphingobium indicum B90A; isolated from two discrete geographical locations, Japan and India, respectively) capable of degrading HCH, with metagenomic data from an HCH dumpsite (∼450 mg HCH per g soil), enabled the reconstruction and validation of the last-common ancestor (LCA) genotype. Mapping the LCA genotype (3128 genes) to the subspecies genomes demonstrated that >20% of the genes in each subspecies were absent in the LCA. This includes two enzymes from the 'upper' HCH degradation pathway, suggesting that the ancestor was unable to degrade HCH isomers, but descendants acquired lin genes by transposon-mediated lateral gene transfer. In addition, anthranilate and homogentisate degradation traits were found to be strain (selectively retained only by UT26) and environment (absent in the LCA and subspecies, but prevalent in the metagenome) specific, respectively. One draft secondary chromosome, two near complete plasmids and eight complete lin transposons were assembled from the metagenomic DNA. Collectively, these results reinforce the elastic nature of the genus Sphingobium, and describe the evolutionary acquisition mechanism of a xenobiotic degradation phenotype in response to environmental pollution. This also demonstrates for the first time the use of metagenomic data in ancestral genotype reconstruction, highlighting its potential to provide significant insight into the development of such phenotypes