Microbial Identification Using rRNA Operon Region: Database and Tool for Metataxonomics with Long-Read Sequence.

Recent development of long-read sequencing platforms has enabled researchers to explore bacterial community structure through analysis of full-length 16S rRNA gene (∼1,500 bp) or 16S-ITS-23S rRNA operon region (∼4,300 bp), resulting in higher taxonomic resolution than short-read sequencing platforms. Despite the potential of long-read sequencing in metagenomics, resources and protocols for this technology are scarce. Here, we describe MIrROR, the database and analysis tool for metataxonomics using the bacterial 16S-ITS-23S rRNA operon region. We collected 16S-ITS-23S rRNA operon sequences extracted from bacterial genomes from NCBI GenBank and performed curation. A total of 97,781 16S-ITS-23S rRNA operon sequences covering 9,485 species from 43,653 genomes were obtained. For user convenience, we provide an analysis tool based on a mapping strategy that can be used for taxonomic profiling with MIrROR database. To benchmark MIrROR, we compared performance against publicly available databases and tool with mock communities and simulated data sets. Our platform showed promising results in terms of the number of species covered and the accuracy of classification. To encourage active 16S-ITS-23S rRNA operon analysis in the field, BLAST function and taxonomic profiling results with 16S-ITS-23S rRNA operon studies, which have been reported as BioProject on NCBI are provided. MIrROR (http://mirror.egnome.co.kr/) will be a useful platform for researchers who want to perform high-resolution metagenome analysis with a cost-effective sequencer such as MinION from Oxford Nanopore Technologies. IMPORTANCE Metabarcoding is a powerful tool to investigate community diversity in an economic and efficient way by amplifying a specific gene marker region. With the advancement of long-read sequencing technologies, the field of metabarcoding has entered a new phase. The technologies have brought a need for development in several areas, including new markers that long-read can cover, database for the markers, tools that reflect long-read characteristics, and compatibility with downstream analysis tools. By constructing MIrROR, we met the need for a database and tools for the 16S-ITS-23S rRNA operon region, which has recently been shown to have sufficient resolution at the species level. Bacterial community analysis using the 16S-ITS-23S rRNA operon region with MIrROR will provide new insights from various research fields.

Effects of Platycodon grandiflorum on Gut Microbiome and Immune System of Immunosuppressed Mouse.

Platycodon grandiflorum (PG) is a perennial plant that has been used as a traditional remedy to control immune-related diseases. PG was steamed and dried to improve its taste (PGS). The aim of the study was to investigate the effects of PG and PGS (PG-diets) on the gut microbiome and immune system. We treated PG-diets to immunosuppressed mice via cyclophosphamide (CPA) injection. After two weeks of the supplement, we evaluated specific genera related to body weight and serum immunoglobulin levels and analyzed 16S rRNA sequencing and metagenomics statistical analysis. PG-diets groups showed an increased abundance of microorganisms in immunodeficient mice compared to the control group (NC). Moreover, Akkermansia significantly decreased in response to the CPA in the NC group at the genus level, whereas its abundance increased in the PG-diets groups. We also found that the modulation of the gut microbiome by PG-diets was correlated with body weight, IgA, and IgM levels. The results demonstrate that PG-diets may improve the health benefits of immunosuppressed mice by altering the gut microbiome, though not much difference was found between PG and PGS treatments. Finally, this is the first study showing the effects of PGS-diets on the gut microbiome and immune system as a potential nourishing immunity supplement.

Complete Genome of Lactobacillus iners KY Using Flongle Provides Insight Into the Genetic Background of Optimal Adaption to Vaginal Econiche.

Despite the importance of Lactobacillus iners and its unique characteristics for the study of vaginal adaption, its genome and genomic researches for identifying molecular backgrounds of these specific phenotypes are still limited. In this study, the first complete genome of L. iners was constructed using a cost-effective long-read sequencing platform, Flongle from Oxford Nanopore, and comparative genome analysis was conducted using a total of 1,046 strain genomes from 10 vaginal Lactobacillus species. Single-molecule sequencing using Flongle effectively resolved the limitation of the 2nd generation sequencing technologies in dealing with genomic regions of high GC contents, and comparative genome analysis identified three potential core genes (INY, ZnuA, and hsdR) of L. iners which was related to its specific adaption to the vaginal environment. In addition, we performed comparative prophage analysis for 1,046 strain genomes to further identify the species specificity. The number of prophages in L. iners genomes was significantly smaller than other vaginal Lactobacillus species, and one of the specific genes (hsdR) was suggested as the means for defense against bacteriophage. The first complete genome of L. iners and the three specific genes identified in this study will provide useful resources to further expand our knowledge of L. iners and its specific adaption to the vaginal econiche.

Calcium Montmorillonite-Based Dietary Supplement Attenuates Necrotic Enteritis Induced by Eimeria maxima and Clostridium perfringens in Broilers.

Necrotic enteritis (NE) is a poultry disease caused by Clostridium perfringens and characterized by severe intestinal necrosis. The incidence of avian NE has been progressively increasing following the removal of antibiotics from poultry feed. We evaluated the effect of diets supplemented with the thermally-processed clays, calcium montmorillonite (CaMM) on clinical signs, immunopathology, and cytokine responses in broiler chickens using an experimental model of NE consisting of co-infection with Eimeria maxima and C. perfringens. In Trial 1, Ross/Ross chickens were fed from hatch with a normal basal diet or a CaMM-supplemented diet with or without a fermentable fiber, an organic acid, and/or a plant extract, and co-infected with E. maxima and C. perfringens under conditions simulating clinical infection in the field. Chickens fed a diet supplemented with CaMM plus a fermentable fiber and an organic acid had increased body weight gain, reduced gut lesions, and increased serum antibody levels to C. perfringens α-toxin and NetB toxin compared with chickens fed the basal diet alone. Levels of transcripts for interleukin-1ß (IL-1ß), IL-6, inducible nitric oxide synthase, and tumor necrosis factor-α superfamily-15 were significantly altered in the intestine and spleen of CaMM-supplemented chickens compared with unsupplemented controls (p<0.05). In Trial 2, Cobb/Cobb chickens were fed an unsupplemented diet or a diet supplemented with CaMM or Varium®, each with a fermentable fiber and an organic acid, and co-infected with E. maxima and C. perfringens under subclinical infection conditions. Compared with unsupplemented controls, broilers fed with CaMM plus a fermentable fiber and an organic acid had increased body weight gain, and reduced feed conversion ratio, mortality, and intestinal lesions, compared with chickens fed an unsupplemented diet (p<0.05). Dietary supplementation of broiler chickens with CaMM plus a fermentable fiber and an organic acid might be useful to control avian NE in the field.

Immune and anti-oxidant effects of in ovo selenium proteinate on post-hatch experimental avian necrotic enteritis.

This study was conducted to investigate the effects of in ovo administration of selenium (Se) incorporated into hydrolyzed soybean protein (B-Taxim [BT]) on protection against experimental avian necrotic enteritis (NE). Broiler eggs were injected with either 100 µl of PBS alone (BT0), or 20 or 40 µg/egg of BT in PBS (BT20, BT40) at 18 days of embryogenesis. On day 14 post-hatch, the chickens were uninfected or orally infected with 1.0 × 10(4) oocysts of Eimeria maxima (E. maxima). On day 18 post-hatch, E. maxima-infected chickens were orally infected with 1.0 × 10(9) CFU of Clostridium perfringens (C. perfringens). Compared with untreated and infected BT0 controls, BT20 and/or BT40 birds showed increased body weights, decreased fecal shedding of E. maxima oocysts, lower serum α-toxin and NetB levels, increased levels of serum antibodies against C. perfringens α-toxin and NetB toxin, decreased levels of serum malondialdehyde, reduced serum catalase and superoxide dismutase catalytic activities, and increased intestinal levels of gene transcripts encoding interleukin (IL)-1ß, IL-6, IL-8, and peroxiredoxin-6, but decreased levels of transcripts for catalase and glutathione peroxidase. Interestingly, transcript levels for inducible nitric oxide synthase and paraoxonase/arylesterase 2 were decreased in the BT20 group and increased in the BT40 group, compared with BT0 controls. These results indicate that in ovo administration of broiler chickens with a Se-containing protein hydrolysate enhanced protection against experimental NE possibly by altering the expression of proinflammatory and anti-oxidant genes and their downstream pathways.

Development and characterization of mouse monoclonal antibodies reactive with chicken TL1A.

Tumor necrosis factor-like ligand 1A (TL1A) is a type II transmembrane protein predominantly expressed by endothelial cells that promotes the expansion of activated T cells and regulatory T cells, modulates inflammation, and regulates the production of a wide variety of T cell cytokines. However, there have not been any mAbs which specifically detect chTL1A and define its biochemical and immunological properties. So in this study, two mouse monoclonal antibodies (mAbs) which specifically detect chicken TL1A (chTL1A) were developed and characterized. Both mAbs identified a 32 kDa Escherichia coli-derived, poly-histidine-tagged fusion protein by Western blot analysis. The mAbs identified TL1A-secreting cells in the chicken thymus, cecal tonsil, and bursa of Fabricius by immunocytochemistry, and were used to measure serum TL1A levels in normal and necrotic enteritis (NE)-afflicted chickens by antigen capture ELISA. These mAbs inhibited chTL1A-induced spleen lymphocyte proliferation, nitric oxide production by chicken macrophage cells (HD11), and blocked the cytotoxic effect of chTL1A against lymphoblastoid chicken B tumor cells (LSCC-RP9). These new mAbs that detect chTL1A will be important immune reagents for basic and applied research in poultry immunology.