Novel aerobic anoxygenic phototrophic bacterium Jannaschia pagri sp. nov., isolated from seawater around a fish farm.

The genus Jannaschia is one of the representatives of aerobic anoxygenic phototrophic (AAP) bacteria, which is a strictly aerobic bacterium, producing a photosynthetic pigment bacteriochlorophyll (BChl) a. However, a part of the genus Jannaschia members have not been confirmed the photosynthetic ability. The partly presence of the ability in the genus Jannaschia could suggest the complexity of evolutionary history for anoxygenic photosynthesis in the genus, which is expected as gene loss and/or horizontal gene transfer. Here a novel AAP bacterium designated as strain AI_62T (= DSM 115720 T = NBRC 115938 T), was isolated from coastal seawater around a fish farm in the Uwa Sea, Japan. Its closest relatives were identified as Jannaschia seohaensis SMK-146 T (95.6% identity) and J. formosa 12N15T (94.6% identity), which have been reported to produce BChl a. The genomic characteristic of strain AI_62T clearly showed the possession of the anoxygenic photosynthesis related gene sets. This could be a useful model organism to approach the evolutionary mystery of anoxygenic photosynthesis in the genus Jannaschia. Based on a comprehensive consideration of both phylogenetic and phenotypic characteristics, we propose the classification of a novel species within the genus Jannaschia, designated as Jannaschia pagri sp. nov. The type strain for this newly proposed species is AI_62T (= DSM 115720 T = NBRC 115938 T).

Pilot study of a comprehensive resource estimation method from environmental DNA using universal D-loop amplification primers.

Many studies have investigated the ability of environmental DNA (eDNA) to identify the species. However, when individual species are to be identified, accurate estimation of their abundance using traditional eDNA analyses is still difficult. We previously developed a novel analytical method called HaCeD-Seq (haplotype count from eDNA by sequencing), which focuses on the mitochondrial D-loop sequence for eels and tuna. In this study, universal D-loop primers were designed to enable the comprehensive detection of multiple fish species by a single sequence. To sequence the full-length D-loop with high accuracy, we performed nanopore sequencing with unique molecular identifiers (UMI). In addition, to determine the D-loop reference sequence, whole genome sequencing was performed with thin coverage, and complete mitochondrial genomes were determined. We developed a UMI-based Nanopore D-loop sequencing analysis pipeline and released it as open-source software. We detected 5 out of 15 species (33%) and 10 haplotypes out of 35 individuals (29%) among the detected species. This study demonstrates the possibility of comprehensively obtaining information related to population size from eDNA. In the future, this method can be used to improve the accuracy of fish resource estimation, which is currently highly dependent on fishing catches.

Vertical distribution of particle-associated and free-living ammonia-oxidizing archaea in Suruga Bay, a deep coastal embayment of Japan.

We analyzed the vertical distributions of ammonia-oxidizing archaea (AOA) in terms of abundance in Suruga Bay, Japan. We distinguished particle-associated (PA) from free-living (FL) assemblages. According to quantitative PCR measurements of the ammonia monooxygenase subunit A gene (amoA), most marine AOA were in an FL state. The vertical distributions of PA AOA ecotypes differed from the general trend; the Shallow Marine clade was dominant in both the surface and deep layers. Thus, although PA AOA account for a small percentage of AOA abundance, they have a community structure distinct from that of FL AOA in planktonic environments. Marine particles should be investigated further as an unexplored niche of AOA in the ocean.

Amylibacter kogurei sp. nov., a novel marine alphaproteobacterium isolated from the coastal sea surface microlayer of a marine inlet.

A novel Gram-negative bacterium, designated 4G11T, was isolated from the sea surface microlayer of a marine inlet. On the basis of 16S rRNA gene sequence analysis, the strain showed the closest similarity to Amylibacter ulvae KCTC 32465T (99.0 %). However, DNA-DNA hybridization values showed low DNA relatedness between strain 4G11T and its close phylogenetic neighbours, Amylibacter marinus NBRC 110140T (8.0±0.4 %) and Amylibacter ulvae KCTC 32465T (52.9±0.9 %). Strain 4G11T had C18 : 1, C16 : 0 and C18 : 2 as the major fatty acids. The only isoprenoid quinone detected for strain 4G11T was ubiquinone-10. The major polar lipids were phosphatidylglycerol, phosphatidylcholine, one unidentified polar lipid, one unidentified phospholipid and one unidentified aminolipid. The DNA G+C content of strain 4G11T was 50.0 mol%. Based on phenotypic and chemotaxonomic characteristics and analysis of the 16S rRNA gene sequence, the novel strain should be assigned to a novel species, for which the name Amylibacter kogurei sp. nov. is proposed. The type strain of Amylibacter kogurei is 4G11T (KY463497=KCTC 52506T=NBRC 112428T).

Algibacter aquaticus sp. nov., a slightly alkaliphilic marine Flavobacterium isolated from coastal surface water.

A rod-shaped, pale yellow-pigmented, aerobic, Gram-staining-negative strain with gliding motility, designated as strain SK-16T, was isolated from the coastal surface water of a semi-enclosed coastal inlet in Misaki, Japan. Analysis of 16S rRNA gene sequences revealed that SK-16T represented a member of the family Flavobacteriaceae and was closely related to the genus Algibacter, with sequence similarities ranging from 95.9 to 94.3 % to the type strains of species of the genus Algibacter. The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 0 G and iso-C15 : 0 3-OH. Major polar lipids were phosphatidylethanolamine, an aminophospholipid and an unidentified phospholipid. The DNA G+C content of SK-16T was 32.3 mol% and MK-6 was the only predominant isoprenoid quinone. On the basis of the results of phenotypic, genotypic, chemotaxonomic and phylogenetic studies, it was suggested that SK-16T represents a novel species within the genus Algibacter, with the newly proposed name Algibacteraquaticus. The type strain is SK-16T (=NBRC 110220T=KCTC 32974T).

Abundance and distribution of dimethylsulfoniopropionate degradation genes and the corresponding bacterial community structure at dimethyl sulfide hot spots in the tropical and subtropical pacific ocean.

Dimethylsulfoniopropionate (DMSP) is mainly produced by marine phytoplankton but is released into the microbial food web and degraded by marine bacteria to dimethyl sulfide (DMS) and other products. To reveal the abundance and distribution of bacterial DMSP degradation genes and the corresponding bacterial communities in relation to DMS and DMSP concentrations in seawater, we collected surface seawater samples from DMS hot spot sites during a cruise across the Pacific Ocean. We analyzed the genes encoding DMSP lyase (dddP) and DMSP demethylase (dmdA), which are responsible for the transformation of DMSP to DMS and DMSP assimilation, respectively. The averaged abundance (±standard deviation) of these DMSP degradation genes relative to that of the 16S rRNA genes was 33% ± 12%. The abundances of these genes showed large spatial variations. dddP genes showed more variation in abundances than dmdA genes. Multidimensional analysis based on the abundances of DMSP degradation genes and environmental factors revealed that the distribution pattern of these genes was influenced by chlorophyll a concentrations and temperatures. dddP genes, dmdA subclade C/2 genes, and dmdA subclade D genes exhibited significant correlations with the marine Roseobacter clade, SAR11 subgroup Ib, and SAR11 subgroup Ia, respectively. SAR11 subgroups Ia and Ib, which possessed dmdA genes, were suggested to be the main potential DMSP consumers. The Roseobacter clade members possessing dddP genes in oligotrophic subtropical regions were possible DMS producers. These results suggest that DMSP degradation genes are abundant and widely distributed in the surface seawater and that the marine bacteria possessing these genes influence the degradation of DMSP and regulate the emissions of DMS in subtropical gyres of the Pacific Ocean.

Fabibacter misakiensis sp. nov., a marine bacterium isolated from coastal surface water.

A slightly curved-rod-shaped, pink-pigmented, Gram-stain-negative, aerobic bacterial strain with gliding motility, designated SK-8T, was isolated from coastal surface water of Misaki, Japan. Phylogenetic trees generated using 16S rRNA gene sequences revealed that strain SK-8T belonged to the genus Fabibacter and showed 96.0 % sequence similarity to the type strain of the most closely related species, Fabibacter pacificus DY53T. The novel isolate was phenotypically and physiologically different from previously described strains. The major cellular fatty acids were iso-C15 : 1 G, iso-C15 : 0 and iso-C17 : 0 3-OH. Major polar lipids were phosphatidylethanolamine, two aminophospholipids and an unidentified phospholipid. The DNA G+C content was 39.1 mol% and MK-7 was the only predominant isoprenoid quinone. On the basis of this taxonomic study employing a polyphasic approach, it was suggested that strain SK-8T represents a novel species of the genus Fabibacter, with the newly proposed name Fabibacter misakiensis sp. nov. The type strain is SK-8T ( = NBRC 110216T = KCTC 32969T).

The impact of tetrodotoxin (TTX) on the gut microbiome in juvenile tiger pufferfish, Takifugu rubripes.

Tetrodotoxin (TTX) is a potent neurotoxin that accumulates in Takifugu rubripes, commonly known as pufferfish, through the ingestion of TTX-bearing organisms as part of their food chain. Although researchers believe that pufferfish use TTX to relieve stress, data are not currently available on how TTX affects the gut microbiota of pufferfish. To address this gap, our study aimed to investigate whether administering TTX to fish could alter their gut microbiota and overall health under various salinity conditions, including 30.0 ppt, 8.5 ppt, and 1.7 ppt salinity, which represent full-strength, isosmotic, and low-salinity stress, respectively. We analyzed the effect of TTX ingestion on the community structure, core microbiome, and metabolic capabilities of the gut microbiome using high-throughput sequencing technologies. The predominant bacterial taxa within the gut microbiome were Firmicutes (21-85%), Campilobacterota (2.8-67%), Spirochaetota (0.5-14%), and Proteobacteria (0.7-9.8%), with Mycoplasma, uncultured Arcobacteraceae, Brevinema, Vibrio, Rubritalea, and uncultured Pirellulaceae as core genera. Our findings indicated that the impact of TTX on high-abundance genera at 30.0 ppt and 8.5 ppt salinity levels was negligible, indicating their stability and resilience to TTX ingestion. However, at 1.7 ppt, TTX-fed fish showed a significant increase in uncultured Arcobacteraceae. Furthermore, our analysis of TTX-fed fish revealed taxonomic alterations in low-abundance taxa, which altered the predicted functions of the gut microbiota at all salinity levels. These results suggest that TTX administration could cause subtle effects on the metabolic functions of gut microbial communities. Overall, our study provides insights into the complex relationship between a TTX-accumulating animal, T. rubripes, and its gut microbiota.

Bacterial contribution to dissolved organic matter in eutrophic Lake Kasumigaura, Japan.

Incubation experiments using filtered waters from Lake Kasumigaura were conducted to examine bacterial contribution to a dissolved organic carbon (DOC) pool. Bacterial abundance, bacterial production, concentrations of DOC, total dissolved amino acids (TDAA), and total dissolved neutral sugars (TDNS) were monitored during the experiments. Bacterial production during the first few days was very high (20 to 35 µg C liter(-1) day(-1)), accounting for 40 to 70% of primary production. The total bacterial production accounted for 34 to 55% of the DOC loss during the experiment, indicating high bacterial activities in Lake Kasumigaura. The DOC degradation was only 12 to 15%, whereas the degradation of TDAA and TDNS ranged from 30 to 50%, suggesting the preferential usage of TDAA and TDNS. The contribution of bacterially derived carbon to a DOC pool in Lake Kasumigaura was estimated using d-amino acids as bacterial biomarkers and accounted for 30 to 50% of the lake DOC. These values were much higher than those estimated for the open ocean (20 to 30%). The ratio of bacterially derived carbon to bulk carbon increased slightly with time, suggesting that the bacterially derived carbon is more resistant to microbial degradation than bulk carbon. This is the first study to estimate the bacterial contribution to a DOC pool in freshwater environments. These results indicate that bacteria play even more important roles in carbon cycles in freshwater environments than in open oceans and also suggests that recent increases in recalcitrant DOC in various lakes could be attributed to bacterially derived carbon. The potential differences in bacterial contributions to dissolved organic matter (DOM) between freshwater and marine environments are discussed.

Distribution and survival strategies of endemic and cosmopolitan diazotrophs in the Arctic Ocean.

Dinitrogen (N2) fixation is the major source of reactive nitrogen in the ocean and has been considered to occur specifically in low-latitude oligotrophic oceans. Recent studies have shown that N2 fixation also occurs in the polar regions and thus is a global process, although the physiological and ecological characteristics of polar diazotrophs are not yet known. Here, we successfully reconstructed diazotroph genomes, including that of cyanobacterium UCYN-A (Candidatus 'Atelocyanobacterium thalassa'), from metagenome data corresponding to 111 samples isolated from the Arctic Ocean. These diazotrophs were highly abundant in the Arctic Ocean (max., 1.28% of the total microbial community), suggesting that they have important roles in the Arctic ecosystem and biogeochemical cycles. Further, we show that diazotrophs within genera Arcobacter, Psychromonas, and Oceanobacter are prevalent in the <0.2 µm fraction in the Arctic Ocean, indicating that current methods cannot capture their N2 fixation. Diazotrophs in the Arctic Ocean were either Arctic-endemic or cosmopolitan species from their global distribution patterns. Arctic-endemic diazotrophs, including Arctic UCYN-A, were similar to low-latitude-endemic and cosmopolitan diazotrophs in genome-wide function, however, they had unique gene sets (e.g., diverse aromatics degradation genes), suggesting adaptations to Arctic-specific conditions. Cosmopolitan diazotrophs were generally non-cyanobacteria and commonly had the gene that encodes the cold-inducible RNA chaperone, which presumably makes their survival possible even in deep, cold waters of global ocean and polar surface waters. This study shows global distribution pattern of diazotrophs with their genomes and provides clues to answering the question of how diazotrophs can inhabit polar waters.

Photosynthetic characteristics of marine aerobic anoxygenic phototrophic bacteria Roseobacter and Erythrobacter strains.

A coastal Roseobacter strain of marine aerobic anoxygenic phototrophic bacteria (AAnPB) was isolated and phylogenetically determined. The strain OBYS 0001 was characterized by its physiological and biochemical properties with reference to the Erythrobacter longus type strain NBRC 14126. When grown in batch cultures, the growth curves of the both strains were similar. Cellular bacteriochlorophyll a concentrations of the strains reached the maxima in the stationary growth conditions. In vivo fluorescence excitation/optical density spectra between 470 and 600 nm for OBYS 0001 represented higher values than NBRC 14126. Variable fluorescence measurements revealed that the functional absorption cross section (σ) of the bacterial photosynthetic complexes for OBYS 0001 was significantly higher than that for NBRC 14126 under green excitation. These results suggest that Roseobacter can capture green light more efficiently than Erythrobacter for photosynthesis. The photochemical quantum efficiencies (F (v)/F (m)) of the bacterial photosynthetic complexes for OBYS 0001 were consistently lower than those for NBRC 14126. A relationship between the growth rate and F (v)/F (m) was significant for OBYS 0001, but that was not found for NBRC 14126. These results suggested that F (v)/F (m) for AAnPB could not be used as a proxy of the growth rate which is consistent with their mostly heterotrophic characters.

Curcumin improves the survival rate after a massive hepatectomy in rats.

BACKGROUND/AIMS: Curcumin possesses anti-inflammatory and antioxidant effects. Curcumin pretreatment provided a hepatoprotective effect in rat models of chemically-induced hepatotoxicities and ischemia/reperfusion injuries. In this study, we examined whether curcumin could improve the survival rate of rats undergoing a 90% hepatectomy. METHODOLOGY: Rats were administered 340 mg/kg oral curcumin formulated with phosphatidylcholine (curcumin group) or vehicle (control group) for 7 consecutive days and 2 hours prior to the massive hepatectomy. RESULTS: Six of the 13 rats pretreated with curcumin survived, whereas all 13 rats pretreated with vehicle died within day 2 following a massive hepatectomy. A histological examination showed the lobular structure to be disturbed in the rats pretreated with vehicle, whereas the hepatic lobular structure remained relatively stable without necrosis in the rats pretreated with curcumin. The contents of heme oxygenase-1 (HO-1) protein in the control group were low in the preoperative phase. In contrast, the levels of HO-1 protein in the curcumin group were high at the preoperative phase, and thereafter remained at high levels until day 7 following surgery. CONCLUSIONS: Our results suggest that curcumin improves the survival rate by increasing the antioxidant activity in rats after a massive hepatectomy.

Differing growth responses of major phylogenetic groups of marine bacteria to natural phytoplankton blooms in the western North Pacific Ocean.

Growth and productivity of phytoplankton substantially change organic matter characteristics, which affect bacterial abundance, productivity, and community structure in aquatic ecosystems. We analyzed bacterial community structures and measured activities inside and outside phytoplankton blooms in the western North Pacific Ocean by using bromodeoxyuridine immunocytochemistry and fluorescence in situ hybridization (BIC-FISH). Roseobacter/Rhodobacter, SAR11, Betaproteobacteria, Alteromonas, SAR86, and Bacteroidetes responded differently to changes in organic matter supply. Roseobacter/Rhodobacter bacteria remained widespread, active, and proliferating despite large fluctuations in organic matter and chlorophyll a (Chl-a) concentrations. The relative contribution of Bacteroidetes to total bacterial production was consistently high. Furthermore, we documented the unexpectedly large contribution of Alteromonas to total bacterial production in the bloom. Bacterial abundance, productivity, and growth potential (the proportion of growing cells in a population) were significantly correlated with Chl-a and particulate organic carbon concentrations. Canonical correspondence analysis showed that organic matter supply was critical for determining bacterial community structures. The growth potential of each bacterial group as a function of Chl-a concentration showed a bell-shaped distribution, indicating an optimal organic matter concentration to promote growth. The growth of Alteromonas and Betaproteobacteria was especially strongly correlated with organic matter supply. These data elucidate the distinctive ecological role of major bacterial taxa in organic matter cycling during open ocean phytoplankton blooms.

The impact of the intra-abdominal space on liver regeneration after a partial hepatectomy in rats.

BACKGROUND: Little is known about the relationship between intra-abdominal space and liver regeneration. The present study was experimentally designed to investigate the influence of the "occupied space" or the "loss of occupied space" on a regenerating liver. METHODS: Experiment 1: Rats were randomly assigned to two groups: SO (space occupied) rats (n = 40); occupancy of intra-abdominal space followed by a two-thirds partial hepatectomy (PH) and control rats (n = 40); A PH alone. The rats in both groups were euthanized at 24, 48, 96, and 168 h after the operation. Computed tomography (CT) images were analyzed to evaluate the regenerating-direction and the shape of the regenerated remnant liver. The liver to body weight ratio and the proliferating cell nuclear antigen (PCNA) labeling index were measured at each time point. Experiment 2: A second laparotomy was performed at 168 h after the PH in both groups; occupier-removal for the SO rats and a sham operation for the control rats. The rats in both groups were euthanized at 24 and 168 h after the second operation. The liver to body weight ratio and PCNA labeling index were measured at each time point. RESULTS: Experiment 1: The remnant liver of the SO rats enlarged toward the dorsal and caudal side because liver regeneration toward the ventral side in the SO rats was inhibited with the occupier in the abdominal space at 96 h, and later, after the PH. CT images showed a statistically significant difference in the shape of the regenerated remnant liver between the control group and the SO group. The liver/body weight ratio was significantly decreased in the SO rats at 96 and 168 h after PH (P < 0.05). There was no significant difference between the groups in the PCNA labeling index. The SO rats showed a significant increase of the PCNA labeling of the inferior right lobe (10.6%) in comparison with the index of the superior right lobe (7.8%), which came in direct contact with the occupier, at 96 h after the operation (P < 0.05). The cell density of superior right lobe of the SO rats group was significantly higher than that of the control group at 168 h after operation (P < 0.05). Experiment 2: There was no statistically significant difference in the liver/body weight ratio at 168 hrs after the second operation between the groups. However, there was a statistically significant increase of the PCNA labeling index 24 h after the second operation in the occupier-removal rats in comparison with the control rats (P < 0.05). CONCLUSION: The occupied intra-abdominal space was therefore found to suppress liver regeneration after a partial hepatectomy, while the removal of such an occupied space stimulated the regeneration of the liver.

Ex vivo hepatic venography for hepatocellular carcinoma in livers explanted for liver transplantation.

BACKGROUND: Hepatocellular carcinoma (HCC) is supposed to have a venous drainage system to a portal vein, which makes intrahepatic metastasis possible. However, the mechanism of extrahepatic recurrence, including the possibility of a direct route to the systemic circulation from the HCC nodules, remains unclear. Therefore, we performed retrograde hepatic venography for HCC in livers that had been explanted for liver transplantation in order to explore the possible direct connection between the hepatic vein and HCC nodules. METHODS: Of 105 living-donor liver transplantations (LDLT) performed up to July, 2009 at the Department of Surgery, Nagasaki University Hospital, dynamic hepatic venography was performed with contrast media under fluoroscopy for the most recent 13 cases with HCC. The presence of a tumor stain for each HCC case was evaluated and compared with the histological findings of HCC. RESULTS: Hepatic venography revealed a tumor stain in 2 of 13 cases (15%). Neither showed any microscopic tumor invasion of HCC into the hepatic vein. In the other 11 cases, there were 4 microscopic portal venous invasions and 2 microscopic hepatic venous invasions. No patients have shown HCC recurrence in follow-up (median period, 13 months). CONCLUSION: Using ex vivo hepatic venography, a direct connection to the hepatic vein from HCC in whole liver was revealed in 2 cases without demonstrated histopathological invasion to hepatic vein for the first time in the literature. The finding suggests that there is direct spillage of HCC cells into the systemic circulation via hepatic vein.

Draft Genome Sequence of the Aerobic Anoxygenic Phototrophic Bacterium Roseobacter sp. Strain OBYS 0001, Isolated from Coastal Seawater in Otsuchi Bay, Japan.

Here, we report the draft genome sequence of the aerobic anoxygenic phototrophic bacterium Roseobacter sp. strain OBYS 0001, isolated from coastal seawater in Ostuchi Bay, Japan. This genome sequence could be useful for our understanding of the variation in photosynthesis-related genes among aerobic anoxygenic phototrophs.

Management of fungal colonization and infection after living donor liver transplantation.

BACKGROUND/AIMS: Control of infection is important in liver transplant patients under immunosuppressive conditions. In particular, invasive fungal infection is often fatal if diagnosis and therapy are delayed. The aim of this study was to analyze the incidence of fungal colonization and infection after living donor liver transplantation (LDLT). METHODOLOGY: Retrospective analysis was performed with 60 consecutive adult recipients of LDLT. RESULTS: Fungi were isolated from specimens of 16 (26.7%) patients after LDLT. All the fungi were Candida species. One patient for whom Candida species were isolated in ascites and blood was complicated with systemic methicillin-resistant Staphylococcus aureus and cytomegalovirus infection. In the univariate analysis, fungal carriage before surgery (p = 0.01) was associated with fungal isolation after LDLT. In the multivariate analysis, fungal carriage was found to be an independent predictor of fungal isolation (odds ratio: 15.7, p = 0.03). Of the 60 recipients, 16 (26.7%) showed serum levels of beta-D glucan above 60 pg/ml after surgery. Among these, 4 died and were all complicated with severe bacterial infection. CONCLUSION: Preoperative fungal carriage was associated with fungal isolation after LDLT. If fungal infection was suspected after LDLT, along with treatment against fungi, control of complicated infections with other pathogens to be simultaneously considered.

A combination procedure with thrombolytic therapy and balloon dilatation for portal vein thrombus enables the successful performance of antiviral therapy after a living-donor liver transplantation: report of a case.

This report presents a case of portal vein thrombosis possibly caused by anastomotic stricture after living-donor liver transplantation. The patient underwent systemic thrombolytic therapy with tissue plasminogen activator and subsequent balloon dilatation of the stenotic lesion, and both were successful. These procedures allowed the patient to receive antiviral therapy to improve the pancytopenia, leading to a sustained virological response.

Distribution of Dimethylsulfoniopropionate Degradation Genes Reflects Strong Water Current Dependencies in the Sanriku Coastal Region in Japan: From Mesocosm to Field Study.

Dimethyl sulfide (DMS) is an important component of the global sulfur cycle as it is the most abundant sulfur compound that is emitted via the ocean surface to the atmosphere. Dimethylsulfoniopropionate (DMSP), the precursor of DMS, is mainly produced by phytoplankton and is degraded by marine bacteria. To reveal the role of bacteria in the regulation of DMSP degradation and DMS production, mesocosm and field studies were performed in the Sanriku Coast on the Pacific Ocean in northeast Japan. The responsible bacteria for the transformation of DMSP to DMS and the assimilation of DMSP were monitored, and the genes encoding DMSP lyase (dddD and dddP) and DMSP demethylase (dmdA) were analyzed. The mesocosm study showed that the dmdA subclade D was the dominant DMSP degradation gene in the free-living (FL) and particle-associated (PA) fractions. The dddD gene was found in higher abundance than the dddP gene in all the tested samples. Most importantly, DMS concentration was positively correlated with the abundance of the dddD gene. These results indicated that bacteria possessing dmdA and dddD genes were the major contributors to the DMSP degradation and DMS production, respectively. The genes dmdA subclade D and dddP were abundant in the Tsugaru Warm (TW) Current, while the dmdA subclade C/2 and dddD genes were dominant in the Oyashio (OY) Current. Functional gene network analysis also showed that the DMSP degradation genes were divided into OY and TW Current-related modules, and genes sharing similar functions were clustered in the same module. Our data suggest that environmental fluctuations resulted in habitat filtering and niche partitioning of bacteria possessing DMSP degradation genes. Overall, our findings provide novel insights into the distribution and abundance of DMSP degradation genes in a coastal region with different water current systems.

Multicentric occurrence and spread of hepatocellular carcinoma in whole explanted end-stage liver.

AIM: Hepatocellular carcinoma (HCC) arising from the end stages of liver cirrhosis is a fair indication for liver transplantation (LT). To pathologically investigate the multicentric occurrence of relatively early staged HCC in cirrhosis, we studied whole explanted livers. METHODS: Fourteen explanted livers from patients undergoing living donor LT (LDLT) were examined. The stage of the HCCs was judged to be within the Milan criteria (M-C; a single HCC less than 5 cm or three HCCs less than 3 cm). Histological examination was performed using serially sectioned specimens 5-7 mm in width. Characterization of preoperatively detectable and undetectable lesions was also performed. RESULTS: In nine patients (64.3%), a total of 34 nodules were found after whole liver histological examination (WLHE). In five patients (31%), the results exceeded the M-C. The characteristics of undetectable HCCs included a minute (median size 6 mm), well-differentiated appearance (80%), with indistinct margins (85.3%) and without vascular invasion (94%). There was no recurrence in any patients at the time of follow up (median follow-up period, 30.1 months). CONCLUSION: A multicentric occurrence of HCCs was demonstrated in cirrhotic livers with HCCs within the M-C. Undetectable HCCs in cirrhotic livers may have no impact on recurrence after LT.