Benchmark of 16S rRNA gene amplicon sequencing using Japanese gut microbiome data from the V1-V2 and V3-V4 primer sets.

BACKGROUND: 16S rRNA gene amplicon sequencing (16S analysis) is widely used to analyze microbiota with next-generation sequencing technologies. Here, we compared fecal 16S analysis data from 192 Japanese volunteers using the modified V1-V2 (V12) and the standard V3-V4 primer (V34) sets to optimize the gut microbiota analysis protocol. RESULTS: QIIME1 and QIIME2 analysis revealed a higher number of unclassified representative sequences in the V34 data than in the V12 data. The comparison of bacterial composition demonstrated that at the phylum level, Actinobacteria and Verrucomicrobia were detected at higher levels with V34 than with V12. Among these phyla, we observed higher relative compositions of Bifidobacterium and Akkermansia with V34. To estimate the actual abundance, we performed quantitative real-time polymerase chain reaction (qPCR) assays for Akkermansia and Bifidobacterium. We found that the abundance of Akkermansia as detected by qPCR was close to that in V12 data, but was markedly lower than that in V34 data. The abundance of Bifidobacterium detected by qPCR was higher than that in V12 and V34 data. CONCLUSIONS: These results indicate that the bacterial composition derived from the V34 region might differ from the actual abundance for specific gut bacteria. We conclude that the use of the modified V12 primer set is more desirable in the 16S analysis of the Japanese gut microbiota.

Characterization of Aquimarina hainanensis isolated from diseased mud crab Scylla serrata larvae in a hatchery.

Mass mortality due to necrosis signs occurred in hatchery-reared zoea stage larvae of the mud crab Scylla serrata in Okinawa, Japan, and a causative bacterium was isolated. In this study, we identified and characterized the bacterium by genome analysis, biochemical properties and pathogenicity. The bacterium was a Gram-negative, non-motile, long rod, forming yellow colonies on a marine agar plate. It grew at 20-33°C (not at 37°C) and degraded chitin and gelatin. Phylogenetic analysis of the 16S rRNA gene sequence identified the bacterium as Aquimarina hainanensis. Genome sequence data obtained from Illumina MiSeq generated 29 contigs with 3.56 Mbp in total length and a G + C content of 32.5%. The predicted 16 chitinase genes, as putative virulence factors, had certain homologies with those of genus Aquimarina. Experimental infection with the bacterium conducted on larvae of four crustacean species, brine shrimp Artemia franciscana, freshwater shrimp Caridina multidentata, swimming crab Portunus trituberculatus and mud crab S. serrata, revealed that this bacterium was highly virulent to these species. The present study suggests that the bacterium caused mass mortality in mud crab seed production was A. hainanensis and can be widely pathogenic to crustaceans.

Conservative treatment for stable low-energy thoracolumbar vertebral fractures in nonfused segments among elderly patients with diffuse idiopathic skeletal hyperostosis: A matched case-control study.

Diffuse idiopathic skeletal hyperostosis (DISH) is the spontaneous osseous fusion of the spine with anterior bridging osteophytes. It is well-known that conservative treatment for vertebral fractures of fused segment among DISH spines is associated with worse clinical outcomes. However, the prognosis of conservatively treated stable vertebral fractures in neighboring nonfused segments among DISH spines is still unknown. The purpose of this study was to analyze the results of conservative treatment of stable low-energy thoracolumbar (TL) vertebral fracture in nonfused segments among patients with DISH lesions.A total of 390 consecutive patients who visited an emergency department by ambulance with spinal trauma between 2013 and 2017 were retrospectively reviewed. The diagnosis of DISH was determined based on fused spinal segments with bridging osteophytes in at least 3 adjacent vertebrae. For each case of stable TL vertebral fractures in nonfused segments of the DISH spine, we identified 2 age-, sex-, and fracture lesion-matched non-DISH controls who underwent conservative treatment for low-energy TL vertebral fractures during the same period.Of the 33 identified cases of TL fractures with DISH, 14 met our inclusion criteria. The bony union rates of the DISH group and control group were 57% and 75% at the 3-month follow-up examination (P = .38) and 69% and 100% at the 6-month follow-up examination (P = .02), respectively. Among the 13 patients with fractures below the TL junction, fused segments were not diagnosable based on the initial standard radiographs of the lumbar spine for 61.5% of patients.Although this study design was exploratory and the sample size was small, our results suggest that with conservative treatment, stable fractures in nonfused segments in the DISH spine might have a worse prognosis than ordinary osteoporotic vertebral fractures. The diagnosis of coexisting DISH lesions can be missed when only radiographs of the lumbar spine are used to determine the diagnosis.

Recurrent femoral shaft fractures in a child with gnathodiaphyseal dysplasia: a case report.

BACKGROUND: Gnathodiaphyseal dysplasia (GDD) is an extremely rare autosomal dominant disease characterized by cemento-osseous lesions in the jawbones, bone fragility, and diaphyseal sclerosis of the tubular bones. Patients with GDD are prone to sustain fractures by minor accidents. Although over 80 cases have been reported, detailed information about the orthopedic treatment of the fractures is limited. CASE PRESENTATION: A 9-year-old Japanese girl with a known history of GDD presented with pain and deformity in the left thigh after a minor fall. She had a displaced transverse fracture in the mid-shaft of the left femur and underwent a closed reduction and external fixation. In the 25th week after the initial surgery, she had another fracture in the left femur at one of the half-pin insertion sites. She underwent an external fixation again. After this operation, the patient sustained another refracture at the same fracture site and one supracondylar fracture at the distant site of the femur. The supracondylar fracture occurred without any triggering activity before beginning a weight-bearing exercise. The supracondylar fracture was successfully treated conservatively, but she sustained two more diaphyseal fractures at half-pin insertion sites one after another. She eventually underwent a revision surgery with a flexible intramedullary nail. At 3 months postoperatively, the fracture was healed and the patient maintained her ambulatory status without further refracture. CONCLUSIONS: Patients with GDD might have narrower safety ranges of biomechanical and physiological drawbacks, which are considered to be acceptable in ordinary cases. The choice of treatment should be aimed at minimizing these negative effects. We recommend intramedullary devise as the first-choice implant for the treatment of isolated femoral shaft fracture in GDD patients in this age group.

Risk factors for spinal cord injury progression after anterior fusion for cervical spine trauma: a retrospective case-control study.

STUDY DESIGN: Single-center, retrospective case-control study. OBJECTIVES: This study aimed to determine the risk factors for progression of neurological symptoms after anterior fusion for cervical spine trauma with no or incomplete spinal cord injury. SETTING: Community-based hospital with an acute care center in Japan. METHODS: We retrospectively reviewed 54 consecutive unstable subaxial cervical spine fracture/dislocation cases that had undergone surgical treatment. A total of 20 patients with no or incomplete spinal cord injury who underwent anterior fusion were identified. Injury characteristics, bony spinal canal diameter (SCD) at the injured level on computed tomography (CT), diagnosis delay of more than 24 h, and other surgery-related parameters were documented as potential risk factors. RESULTS: The study population included 16 male and 4 female patients. The median age was 71.5 (range: 20-88) years. Two cases of SCI progression were identified (AIS E to C5-8 C and AIS D to C5-8 C). Both cases occurred in men who were older than the average age of all the patients. Only delayed diagnosis was significantly associated with the progression of SCI (p = 0.02). SCDs on CT demonstrated a tendency to be smaller than those of cases without progression, but this was not statistically significant (progression: median, 8.1 [7.2-8.9] mm; no progression: median, 10.1 [4.2-12.6] mm; p = 0.21). CONCLUSION: Our results suggested that a delay in diagnosis was associated with neurological progression after ACF. Furthermore, imposing ligamentous flavum might become a compression factor if the diagnosis is delayed.

Penetrating Anorectal Injury Caused by a Wild Boar Attack: A Case Report.

Wild boar attacks have rarely been reported in the medical literature. This is the case of an 83-year-old male farmer who was assaulted from behind by an injured adult wild boar. He presented with hemorrhagic shock after sustaining injuries to the right profunda femoris artery and right sciatic nerve as well as significant soft-tissue injuries, bilateral iliac wing fractures, an open pneumothorax, and an anorectal injury. The anorectal injury was treated with fecal diversion but was complicated by soft-tissue infection in the surrounding dead space. The patient needed multiple operations, including removal of the distal rectum and creation of a permanent colostomy. In this report, we highlighted the characteristics of anorectal trauma caused by a wild boar attack. We conclude that penetrating anorectal injuries caused by this type of attack can be associated with extensive soft-tissue damage despite externally appearing to be simple puncture wounds. Anorectal combat injuries have demonstrated similar extensive surrounding soft-tissue injuries and propensity for infection; therefore, this case supports adopting a similar treatment strategy, that of serial and radical debridement, to treat certain wild boar injuries.

Complete Genome Sequence of the Lytic Giant Bacteriophage pT24 Infecting Tenacibaculum spp., Isolated from a Shrimp Culture Pond.

The lytic bacteriophage pT24, which infects Tenacibaculum spp., was isolated from the water of a whiteleg shrimp (Litopenaeus vannamei) culture pond in Thailand. This giant bacteriophage with myovirus morphology comprised 234,670 bp with 296 predicted genes.