Microbial community profiling of human saliva using shotgun metagenomic sequencing.

Human saliva is clinically informative of both oral and general health. Since next generation shotgun sequencing (NGS) is now widely used to identify and quantify bacteria, we investigated the bacterial flora of saliva microbiomes of two healthy volunteers and five datasets from the Human Microbiome Project, along with a control dataset containing short NGS reads from bacterial species representative of the bacterial flora of human saliva. GENIUS, a system designed to identify and quantify bacterial species using unassembled short NGS reads was used to identify the bacterial species comprising the microbiomes of the saliva samples and datasets. Results, achieved within minutes and at greater than 90% accuracy, showed more than 175 bacterial species comprised the bacterial flora of human saliva, including bacteria known to be commensal human flora but also Haemophilus influenzae, Neisseria meningitidis, Streptococcus pneumoniae, and Gamma proteobacteria. Basic Local Alignment Search Tool (BLASTn) analysis in parallel, reported ca. five times more species than those actually comprising the in silico sample. Both GENIUS and BLAST analyses of saliva samples identified major genera comprising the bacterial flora of saliva, but GENIUS provided a more precise description of species composition, identifying to strain in most cases and delivered results at least 10,000 times faster. Therefore, GENIUS offers a facile and accurate system for identification and quantification of bacterial species and/or strains in metagenomic samples.

Correlation of limestone beds using laser-induced breakdown spectroscopy and chemometric analysis.

Correlation of limestone beds is commonly based on a variety of features, including the age of the bed, the fossil assemblage, internal sedimentary structures, and the relationship to other units in the stratigraphy. This study uses laser-induced breakdown spectroscopy (LIBS) to correlate 16 limestone beds from Kansas, USA, using three multivariate techniques: (1) soft independent modeling of class analogy (SIMCA) classification, (2) a partial least squares regression, 1 variable (PLS-1) model in which the spectra are regressed against a matrix of the indicator variables 1 through 16, and (3) a matching algorithm that consists of a sequence of binary PLS-1 models. Each gravel-sized limestone particle was analyzed by one LIBS shot; ten spectra were averaged into a single spectrum for chemometric analysis. The entire spectrum (198-969 nm wavelength) is used for multivariate analysis; the only preprocessing is averaging. The SIMCA and PLS-1 models fail to discriminate among the beds, which are chemically similar. In contrast, the matching algorithm has a success rate of 95% to 96%, using half of the spectra to train the model and the other half of the spectra to validate it. However, 100% success can be accomplished by accepting the classification of the majority of spectra for a given bed as the correct classification. This study indicates that LIBS can be applied to complex geologic correlation problems and provide rapid, accurate results.

Use of laser induced breakdown spectroscopy in the determination of gem provenance: beryls.

The provenance of gem stones has been of interest to geologists, gemologists, archeologists, and historians for centuries. Laser induced breakdown spectroscopy (LIBS) provides a minimally destructive tool for recording the rich chemical signatures of gem beryls (aquamarine, goshenite, heliodor, and morganite). Broadband LIBS spectra of 39 beryl (Be(3)Al(2)Si(6)O(18)) specimens from 11 pegmatite mines in New Hampshire, Connecticut, and Maine (USA) are used to assess the potential of using principal component analysis of LIBS spectra to determine specimen provenance. Using this technique, beryls from the three beryl-bearing zones in the Palermo #1 pegmatite (New Hampshire) can be recognized. However, the compositional variation within this single mine is comparable to that in beryls from all three states. Thus, a very large database with detailed location metadata will be required to routinely determine gem beryl provenance.

Laser-induced breakdown spectroscopy analysis of complex silicate minerals--beryl.

Beryl (Be3Al2Si6O18) is a chemically complex and highly compositionally variable gem-forming mineral found in a variety of geologic settings worldwide. A methodology and analytical protocol were developed for the analysis of beryl by laser-induced breakdown spectroscopy (LIBS) that minimizes the coefficient of variance for multiple analyses of the same specimen. The parameters considered were laser energy/pulse, time delay and crystallographic orientation. Optimal analytical conditions are a laser energy/pulse of 102 mJ and a time delay of 2 micros. Beryl compositions measured parallel and perpendicular to the c axis were identical within analytical error. LIBS analysis of 96 beryls from 16 countries (Afghanistan, Brazil, Canada, China, Colombia, India, Ireland, Italy, Madagascar, Mexico, Mozambique, Namibia, Norway, Russia, Tanzania and United States), Antarctica, and ten US states (AZ, CA, CO, CT, ID, ME, NC, NH, NM and UT) were undertaken to determine whether or not LIBS analysis can be used to determine the provenance of gem beryl.