.. Acknowledgements The authors wish to thank David Alt, USDA/ARS/National Animal Disease Center for technical advice and the State University CHIR-258 of New York, University at Buffalo Center of Excellence in Bioinformatics and Life Sciences for performing pyrosequencing. This work was supported, in part, by grants from the NIH/NCRR (D.W. Dyer, Grant #P2PRR016478), National Pork Board (G.J. Phillips and D.W. Dyer) and Iowa Healthy Livestock Initiative (G.J. Phillips and K.B. Register).
A representative genomic 16S rRNA sequence of strain MAS10T was compared using NCBI BLAST [3,4] under default settings (e.g., considering only the high-scoring segment pairs (HSPs) from the best 250 hits) with the most recent release of the Greengenes database [5] and the relative frequencies of taxa and keywords (reduced to their stem [6]) were determined, weighted by BLAST scores.
The most frequently occurring genera were Acidithiobacillus (60.0%), Deferribacter (26.8%), Flexistipes (8.2%), Desulfuromonas (2.2%) and Calditerrivibrio (1.8%) (80 hits in total). Regarding the single hit to sequences from members of the species, the average identity within HSPs was 98.0%, whereas the average coverage by HSPs was 96.9%. Among all other species, the one yielding the highest score was Deferribacter abyssi (“type”:”entrez-nucleotide”,”attrs”:”text”:”AJ515881″,”term_id”:”25136921″,”term_text”:”AJ515881″AJ515881), which corresponded to an identity of 89.7% and an HSP coverage of 86.4%. (Note that the Greengenes database uses the INSDC (= EMBL/NCBI/DDBJ) annotation, which is not an authoritative source for nomenclature or classification.
) The highest-scoring environmental sequence was “type”:”entrez-nucleotide”,”attrs”:”text”:”FR744611″,”term_id”:”325504644″,”term_text”:”FR744611″FR744611 (‘succession potential reducers nitrate-treated facility determined temperature and nitrate availability production water Halfdan oil field clone PWB039′), which showed an identity of 96.7% and an HSP coverage of 93.1%. The most frequently occurring keywords within the labels of all environmental samples which yielded hits were ‘microbi’ (3.9%), ‘acid’ (3.4%), ‘sediment’ (3.3%), ‘water’ (3.0%) and ‘oil’ (2.4%) (170 hits in total). The most frequently occurring keyword within the labels of those environmental samples which yielded hits of a higher score than the highest scoring species was ‘avail, determin, facil, field, halfdan, nitrat, nitrate-tr, oil, potenti, product, reduc, success, temperatur, water’ (7.
1%) (1 hit in total). While these keywords fit to the marine environment from which strain MAS10T originated, they also point to sediments and oil fields which were so far not considered as habitats for F. sinusarabici. Figure 1 shows the phylogenetic neighborhood of F. sinusarabici MAS10T in a 16S rRNA based Brefeldin_A tree.