PhyloToAST: Bioinformatics Tools for Species-Level Analysis and Visualization of Complex Microbial Datasets

The 16S rRNA gene is widely used for taxonomic profiling of microbial ecosystems; and recent advances in sequencing chemistry have allowed extremely large numbers of sequences to be generated from minimal amounts of biological samples. Analysis speed and resolution of data to species-level taxa are two important factors in large-scale explorations of complex microbiomes using 16S sequencing. We present here new software, Phylogenetic Tools for Analysis of Species-level Taxa (PhyloToAST), that completely integrates with the QIIME pipeline to improve analysis speed, reduce primer bias (requiring two sequencing primers), enhance species-level analysis, and add new visualization tools. The code is free and open source, and can be accessed at http://phylotoast.org

Dysbiotic Subgingival Microbial Communities in Periodontally Healthy Patients With Rheumatoid Arthritis

Objective: Studies that demonstrate an association between rheumatoid arthritis (RA) and dysbiotic oral microbiomes are often confounded by the presence of extensive periodontitis in these individuals. This study was undertaken to investigate the role of RA in modulating the periodontal microbiome by comparing periodontally healthy individuals with RA to those without RA. Methods: Subgingival plaque was collected from periodontally healthy individuals (22 with RA and 19 without RA), and the 16S gene was sequenced on an Illumina MiSeq platform. Bacterial biodiversity and co‐occurrence patterns were examined using the QIIME and PhyloToAST pipelines. Results: The subgingival microbiomes differed significantly between patients with RA and controls based on both community membership and the abundance of lineages, with 41.9% of the community differing in abundance and 19% in membership. In contrast to the sparse and predominantly congeneric co‐occurrence networks seen in controls, RA patients revealed a highly connected grid containing a large intergeneric hub anchored by known periodontal pathogens. Predictive metagenomic analysis (PICRUSt) demonstrated that arachidonic acid and ester lipid metabolism pathways might partly explain the robustness of this clustering. As expected from a periodontally healthy cohort, Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans were not significantly different between groups; however, Cryptobacterium curtum, another organism capable of producing large amounts of citrulline, emerged as a robust discriminant of the microbiome in individuals with RA. Conclusion: Our data demonstrate that the oral microbiome in RA is enriched for inflammophilic and citrulline‐producing organisms, which may play a role in the production of autoantigenic citrullinated peptides in RA

Distribution of organic carbon in sediments of the north western continental shelf of India

127-129Organic carbon in the sediments varies from 0.24 to 2.42 % (av. 0.95 %) which is far below the world average for the nearshore sediments. Fine grained terrigenous sediments of the shelf off Saurashtra coast and those in the inner shelf between Bombay and Port Dabhol are characterised by relatively high organic carbon content (> 1%); fine grained sediments of the inner shelf between Gulf of Cambay and the shelf between Indus canyon and Gulf of Kutch and the coarse grained carbonate relict sediments on the outer shelf are characterised by low organic carbon content (< 1%). Differences found in the organic carbon contents of the fine grained sediments of different regions can be traced mainly to the differences in the productivity of the overlying waters. Although in the outer shelf regions also, areas of high and low productivity are encountered, the low organic carbon content in these sediments appears to be due to a combination of several factors-coarse grained nature of the sediments, relatively low rate of sedimentation and lack of enough fine grained terrigenous material for the protection and preservation of organic matter in the sediments. The generally low organic carbon content recorded in this area when compared to world average for the shelf sediments, can be attributed to the oxidation because of high dissolved oxygen content of bottom water or grazing by zooplankton and other higher organisms

Multi-Hop Relay Selection Based on Fade Durations

In cooperative relaying, the selection of relays could be based on different parameters. The most well-known and frequently used metric is the signal-to-noise ratio (SNR). In this method of relay selection, the rapid fluctuation of the signal (i.e., fading) is not taken into account in the selection criteria. Such rapid signal change may cause significant loss of information, degrade signal quality for voice or video connections, or could make the channel coding fail. An alternative method of relay selection in a cooperative relay network is by considering fading. Such methods include average fade duration (AFD) and fade duration outage probability (FDOP), which are based on time correlation statistics. Both the AFD and the FDOP are computed in reference to a threshold value for signal quality. This work derives new formulas for two hop and three hop relay paths, with three hop paths given a penalty cost. Then optimization algorithms for each type of relay selection method are derived, including total path and link-by-link optimization. Simulation results provide optimal AFD and FDOP paths for various random network topologies. These paths are then compared to paths that would be found if SNR metrics were used instead. It is shown that SNR optimization results in much different performance. For cases of four sources and four relays, SNR based optimization frequently chose different relay paths, as low as only 63% of the same relay paths as FDOP or AFD optimizations. Because fade duration methods more accurately control the fading nature and true quality of the signals, the results here provide significant improvements in relay performance and allow two and three hop relay paths to be implemented effectively

Distribution Patterns of Aluminium, Titanium, Manganese, Copper and Nickel in Sediments of the Northern Half of the Western Continental Shelf of India

67-71Studies on the distribution patterns of various elements coupled with the distribution pattern of calcium carbonate have revealed that (i) along any given section across the shelf, relatively high concentrations of all the elements are associated with the terrigenous sediments than those with the relict sediments of the outer shelf, (ii) elements like titanium, manganese and copper exhibit regional differences from north to south and (iii) manganese, nickel and copper (on carbonate-free basis) tend to be enriched in clays and silty clays of the outer shelf region. While variations across the shelf are attributed to the association of elements with the terrigenous material to a large extent, variations along the shelf (from north to south) are attributed to the differences in the mineralogical composition of sediments. These studies have also revealed that the effect of Indus river system is profound on the shelf between Indus canyon and Gulf of Kutch, marginal between Gulf of Kutch and Gulf of Cambay and least in the rest of the region

Distribution of Fe, Mn, Ni, Co, Cu and Zn in Non-lithogenous Fractions of Sediments of Gulf of Kutch

54-56Contributions made by non-lithogenous fractions of sediments constitute a significant portion of the concentrations of the elements associated with the total sediment samples. The minor differences found in their distribution patterns can be attributed to compositional differences in the individual samples. From an evaluation of the processes of incorporation of elements into sediments in association with non-lithogenous fractions, it is tentatively concluded that the elements particularly trace elements are incorporated more through adsorption on clays than through other processes. However, the absence of covariance among different elements appears to be due to the differential behaviour of elements in regard to adsorption and desorption as a result of the churning of bottom sediments constantly by tidal bores

Distribution of Al, Mn, Ni, Co and Cu in the Non-lithogenous Fractions of Sediments of the Northern Half of the Western Continental Shelf of India

56-61Higher amounts of elements are associated with the nonlithogenous fractions of the fine grained terrigenous sediments of the innershelf region with low carbonate content than with the corresponding fractions of the coarse grained sediments of the outer shelf region with high calcium carbonate content and all the elements covary with each other in the environment. From an evaluation of the role of different processes with the incorporation of elements, particularly trace elements into the nonlithogenous fractions, it is inferred that in the innershelf region they are incorporated in association with the hydroxide of iron and manganese while in the outer shelf region they are associated with the carbonate phase

Distribution of Phosphate in Sediments of the Northern Half of the Western Continental Shelf of India

146-150The study has revealed that (i) P2O5 content in the sediments varies from 0.17 to 1.2%, (ii) fine grained sediments of terrigenous origin occupying inner shelf region between Gulf of Cambay and Port Dabhol and greater part of the shelf region north of Gulf of Cambay up to Indus Canyon contain low percentages of phosphate ( 0.2 to 0.3%), typical for normal marine sediments, while the relict zone of the outer shelf region between Gulf of Cambay and a little south of Bombay and the upper Continental slope region contain relatively high content of P2O5 and (iii) P2O5 content of the acid soluble fractions of the sediments also exhibits a similar trend. These distribution patterns are discussed in relation to the distribution patterns of the sediments and their chemistry and the hydrographic features of the overlying waters. From these studies, it is suggested that the outer shelf region between Gulf of Cambay and a little south of Bombay and the Continental slope region are environmentally favourable for detailed exploration of phosphate

Partition Studies in the Sediments of Deep Sea Drilling Project Site 220 in the Southeastern Arabian Sea

254-257Partition patterns of Al, Fe, Mn, Ni, Co and Cu have been studied in sediments. These studies have revealed that all the elements have both acid insoluble and non-lithogenous components in these sediments and exhibit differences in their distribution pattern in the sedimentary column. While the concentrations of different elements associated with the acid insoluble fractions are fixed in sediments in a solid state and the differences found can be attributed to differences in the nature of the material the site received during different periods, the concentrations associated with the non-lithogenous component of sediments appear to have been fixed in a number of ways. While Al, Fe and Mn seem to be associated with the clays and carbonate phase, Ni, Co and Cu in sediments appear to have been fixed through adsorption on clays and organic matter and by ferric and manganese hydroxides. Considering the depositional history of the site, rates of sedimentation during different geological periods and the nature of the material deposited, it is tentatively suggested that the differences found in the concentrations of different elements in the nonlithogenous fraction are related to a large extent to differences in rates of sedimentation and to the character of the material in the different lithological units