Iodide-oxidizing bacteria are able to catalyze the oxidation of iodide ion (I⁻) to molecular iodine (I₂), and they have been isolated from natural gas brine water containing very high concentrations (up to 1.2 mM) of iodide. They are aerobic heterotrophic bacteria in the class Alphaproteobacteria and are divided into two phylogenetic groups. One of the groups is most closely related to Roseovarius mucosus, whereas the other group is closely related to the Kordiimonadales and Rhodothalassium salexigens, with relatively low 16S rRNA gene identity levels of 89％ to 91％. Iodide-oxidizing bacteria can also be enriched from natural seawater supplemented with iodide, because their I₂ tolerance is much higher than that of other heterotrophic bacteria in seawater. The enzyme catalyzing the oxidation of iodide (IOX) is an extracellular oxidase; it also has marked activity towards various phenolic compounds, including ABTS, syringaldazine, and 2,6-dimethoxy phenol. Further studies have revealed that IOX is a putative multicopper oxidase (MCO) but is phylogenetically distinct from other known bacterial MCOs such as CueO, CumA, CopA, and CotA. The fact that IOX has the highest catalytic efficiency (k_cat/K_m) for iodide among the known MCOs makes it a suitable candidate for a wide range of applications, including enzyme-based antimicrobial systems and decolorization of recalcitrant dyes.

Repositories of culture collections of Biosafety Level 3 (BSL3) pathogens are expected to provide information on the pathogenic factors present in stock bacteria. However, it is difficult to maintain valid pathogenic information on each of the different BLS3 pathogens because quality control of the stock strains generally has to be performed by a few staff members.

We developed a common platform to differentiate six different PCR amplicons on a DNA strip. The six amplicons can be differentiated with the help of three position markers printed on the strip. With this method, the pathogenic factors in BSL3 pathogens can be determined within 40 min after cultured bacteria are picked up from a single colony.

Phylogenetic analysis was performed by using a concatenation of eight full-length polymorphic genes encoding large hypervariable proteins (designated C8HKP) selected from among 121 housekeeping proteins shared and conserved in Pseudomonas aeruginosa strain PAO1, Pseudomonas fluorescens strain A506, Pseudomonas putida NBRC 14164, Pseudomonas stutzeri ATCC 17588, and Pseudomonas syringae pv. phaseolicola strain 1448A, which were selected from phylogenetically different groups. The results were compared with those of a previously reported phylogenetic analysis that used a multilocus sequence analysis (MLSA) incorporating four housekeeping genes (16S rRNA, gyrB, rpoB, and rpoD; designated 4MLSA). Comparison of the substitution rates between C8HKP and 4MLSA revealed that C8HKP was strongly correlated (R²=0.897) with 4MLSA and had twice the resolving power of 4MLSA. Furthermore, the phylogenetic positions of the genus Pseudomonas were almost identical between the two methods. These results indicate that C8HKP is suitable for phylogenetic analysis of Pseudomonas species. Additionally, C8HKP phylogenetic analysis was performed on draft genome sequences for 33 clinical isolates identified as P. putida group by 16S rRNA gene analysis. The results revealed that several strains belonged to three independent clusters in the P. putida group. Classification of novel species in the P. putida group will therefore be required.

To determine the usefulness of the lactic acid bacteria and staphylococci isolated from Thai fermented foods, we investigated their sugar fermentation ability and functional properties. Lactic acid bacteria fermented a much greater variety of sugars than did Staphylococcus strains. Cluster analysis based on the sugar fermentation patterns of strains isolated from Thai fermented foods showed that most isolates followed the species characteristics, but some lactic acid bacteria showed within-species diversity of sugar fermentation ability. Cluster analysis based on the sugar fermentation patterns of both the Thai food strains and those isolated from Japanese fermented foods showed that most of the species with diverse sugar fermentation patterns were isolated from multiple locations. These results suggest that the fermentation abilities of these strains have diversified easily and that the strains are highly adaptable. Among those species with diverse sugar fermentation patterns, those of the Japanese isolates were found in more than one location, whereas some of those of the Thai isolates were found only in Thailand. Most of the isolates clustered together with the type strain belonged to species found in a single location, and the number of such species was largest in the Thai isolates. Thus the fermentation abilities of the strains isolated from Thai fermented foods differed from those of the Japanese isolates. Some of the lactic acid bacteria isolated produced GABA, and some of the Staphylococcus strains produced protease. The strains isolated from Thai fermented foods are thus unique bioresources.

Four hundred and forty-seven fungal isolates were obtained from ca. 300 specimens of woody plants and some herbs, including their parasites, in the Bonin Islands from 2011 to 2014. Two hundred and eighty-six of the isolates were identified as 124 species and 161 isolates were classified into many genera on the basis of their morphology and the results of a BLASTn search with barcode DNA sequences such as the ITS region of the 18S rRNA gene and the D1/D2 domain of the 28S rRNA gene. Thirty-seven species were new to Japan and 21 species were new to the Bonin Islands. Fifty-seven species were found on 80 new hosts, which included 19 plants endemic to the islands. Although at least 50 other isolates from the endemic hosts were classified into 37 genera, they could not be identified at species level despite the BLASTn search. More studies in detail are needed to identify these isolates, which seemed to be new taxa. Thirteen species new to Japan and a fungus new to the islands, which were isolated from both tropical and subtropical hosts, are known inhabitants of warmer areas of the world. The tropical or subtropical component in the mycobiota of the Bonin Islands was reconfirmed by the present study.

To further catalogue the distribution of cyanobacterial cellular polyamines, we used HPLC and HPGC to newly analyze the acid-extracted polyamines from 14 cyanobacteria. The colony-forming Nostoc verrucosum (“Ashitsuki”) and Nostoc commune (“Ishikurage”), as well as Anabaena species (Nostocales), contained homospermidine. The thermo-halotolerant Spirulina subsalsa var. salina (Spirulinales), as well as freshwater Spirulina strains, contained spermidine. Putrescine, spermidine, and homospermidine were found in freshwater colony-forming Aphanothece sacrum (“Suizenji-nori”), whereas the halotolerant Aphanothece halophytica and Microcystis species (Chroococcales) contained spermidine alone. In addition to putrescine, spermidine, homospermidine and agmatine, thermospermine was found as a major polyamine in haloalkaliphilic Arthrospira platensis (“Spirulina”) (Oscillatoriales). In the Synechococcales, chlorophyll b-containing Prochlorococcus marina contained spermidine, and chlorophyll d-containing Acaryochloris marina contained spermidine and homospermidine. Thermophilic Thermosynechococcus vulcanus and Thermosynechococcus sp. NK55a, as well as Thermosynechococcus elongatus, contained low levels of spermine in addition to homospermidine. The present 14 and previous 126 strains of cyanobacteria were categorized into spermidine-dominant types, homospermidine-dominant types and spermidine-homospermidine-mix types, but their polyamine profiles have not yet been established as chemotaxonomic markers.