Sporosarcina jeotgali sp. nov., Sporosarcina oncorhynchi sp. nov., and Sporosarcina trichiuri sp. nov., Isolated from Jeotgal, a Traditional Korean Fermented Seafood.

Three novel, Gram-stain-positive, obligate aerobic, catalase- and oxidase-positive bacterial strains, designated B2O-1T, T2O-4T, and 0.2-SM1T-5T, were isolated from jeotgal, a traditional Korean fermented seafood. Strains B2O-1T, T2O-4T, and 0.2-SM1T-5T exhibited distinct colony colors, characterized by pink, yellow, and red opaque circular colonies, respectively. Phylogenetic analysis revealed that three strains formed a paraphyletic clade within the genus Sporosarcina and shared < 99.0% similarity with Sporosarcina aquimarina KCTC 3840T and Sporosarcina saromensis KCTC 13119T in their 16S rRNA gene sequences. The three strains exhibiting Orthologous Average Nucleotide Identity values < 79.3% and digital DNA-DNA hybridization values < 23.1% within the genus Sporosarcina affirmed their distinctiveness. Strains B2O-1T, T2O-4T, and 0.2-SM1T-5T contained MK-7 as a sole respiratory menaquinone and A4α type peptidoglycan based on lysine with alanine, glutamic acid, and aspartic acid. The common polar lipids include diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. Strain T2O-4T contained one unidentified phospholipid, whereas strain 0.2-SM1T-5T contained two unidentified phospholipids. Cellular fatty acid profiles, with C15:0 anteiso as the major fatty acid, supported the affiliation of the three strains to the genus Sporosarcina. Based on the polyphasic characteristics, strains B2O-1T (= KCTC 43506T = JCM 36032T), T2O-4T (= KCTC 43489T = JCM 36031T), and 0.2-SM1T-5T (= KCTC 43519T = JCM 36034T) represent three novel species within the genus Sporosarcina, named Sporosarcina jeotgali sp. nov., Sporosarcina oncorhynchi sp. nov., and Sporosarcina trichiuri sp. nov., respectively.

Genomic attributes and characterization of novel exopolysaccharide-producing bacterium Halomonas piscis sp. nov. isolated from jeotgal.

Halophilic bacterial strains, designated SG2L-4T, SB1M4, and SB2L-5, were isolated from jeotgal, a traditional Korean fermented food. Cells are Gram-stain-negative, aerobic, non-motile, rod-shaped, catalase-positive, and oxidase-negative. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain SG2L-4T is closely related to Halomonas garicola KACC 18117T with a similarity of 96.2%. The complete genome sequence of strain SG2L-4T was 3,227,066 bp in size, with a genomic G + C content of 63.3 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain SG2L-4T and H. garicola KACC 18117T were 90.5 and 40.7%, respectively. The optimal growth conditions for strain SG2L-4T were temperatures between 30 and 37°C, a pH value of 7, and the presence of 10% (w/v) NaCl. The polar lipids identified included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unknown phospholipid, an unknown glycolipid, and an unknown polar lipid. The major cellular fatty acids were C16:0, summed features 8 (C18:1ω6c and/or C18:1ω7c), C19:0 cyclo ω8c, and summed features 3 (C16:1ω6c and/or C16:1ω7c). The predominant respiratory quinone was ubiquinone with nine isoprene units (Q-9). Based on the phenotypic, genotypic, and chemotaxonomic results, strain SG2L-4T represents a novel species within the genus Halomonas, for which the name Halomonas piscis sp. nov. is proposed. The type strain is SG2L-4T (=KCTC 92842T = JCM 35929T). Functional annotation of the genome of strain SG2L-4T confirmed the presence of exopolysaccharide synthesis protein (ExoD) and capsular polysaccharide-related genes. Strain SG2L-4T also exhibited positive results in Molisch's test, indicating the presence of extracellular carbohydrates and exopolysaccharides (EPS) production. These findings provide valuable insights into the EPS-producing capabilities of H. piscis sp. nov. isolated from jeotgal, contributing to understanding its potential roles in food and biotechnological applications.

Alkalimarinus alittae sp. nov., isolated from gut of marine sandworm (Alitta virens) and emended description of the genus Alkalimarinus.

A novel, Gram-stain-negative, aerobic, motile, catalase- and oxidase-negative bacterial strain, designated A2M4T, was isolated from the gut contents of a marine sandworm Alitta virens, collected from the eastern coast of the Republic of Korea. Strain A2M4T formed translucent circular colonies and showed rod-shaped cells with peritrichous flagella. Optimal growth of strain A2M4T occurred at 25 °C, pH 7.0 and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain A2M4T was closely related to Alkalimarinus sediminis FA028T, with the highest sequence similarity of 98.9 %. The complete genome sequence of strain A2M4T was 4.25 Mbp in size and the genomic G+C content, calculated from the genome sequence, was 43.2 mol%. A comparison between the genome sequence of strain A2M4T and that of its closest relative, A. sediminis FA028T, showed an average nucleotide identity value of 76.63 % and a digital DNA-DNA hybridization value of 22.2 %. Strain A2M4T contained Q-9 as the sole respiratory isoprenoid quinone and the major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acids of strain A2M4T were C14 : 0, C16 : 0 and summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c). Based on its phenotypic, chemotaxonomic and genomic characteristics, strain A2M4T represents a novel species of the genus Alkalimarinus, for which the name Alkalimarinus alittae sp. nov. is proposed. The type is strain A2M4T (=KCTC 92030T=JCM 35924T). The description of the genus Alkalimarinus has also been emended.

Risk factors associated with death due to severe fever with thrombocytopenia syndrome in hospitalized Korean patients (2018-2022).

BACKGROUND: Severe fever with thrombocytopenia syndrome (SFTS) has no vaccine or treatment and an extremely high fatality rate. We aimed to analyze and evaluate the risk factors for death associated with SFTS. METHODS: Among reports from 2018 to 2022, we compared and analyzed 1,034 inpatients aged 18 years or older with laboratory-confirmed SFTS who underwent complete epidemiological investigations. RESULTS: Most of the inpatients with SFTS were aged 50 years or older (average age, 67.6 years). The median time from symptom onset to death was 9 days, and the average case fatality rate was 18.5%. Risk factors for death included age of 70 years or older (odds ratio [OR], 4.82); agriculture-related occupation (OR, 2.01); underlying disease (OR, 7.20); delayed diagnosis (OR, 1.28 per day); decreased level of consciousness (OR, 5.53); fever/chills (OR, 20.52); prolonged activated partial thromboplastin time (OR, 4.19); and elevated levels of aspartate aminotransferase (OR, 2.91), blood urea nitrogen (OR, 2.62), and creatine (OR, 3.21). CONCLUSION: The risk factors for death in patients with SFTS were old age; agriculture-related occupation; underlying disease; delayed clinical suspicion; fever/chills; decreased level of consciousness; and elevated activated partial thromboplastin time, aspartate aminotransferase, blood urea nitrogen, and creatine levels.

Host phylogeny, habitat, and diet are main drivers of the cephalopod and mollusk gut microbiome.

BACKGROUND: Invertebrates are a very attractive subject for studying host-microbe interactions because of their simple gut microbial community and host diversity. Studying the composition of invertebrate gut microbiota and the determining factors is essential for understanding their symbiotic mechanism. Cephalopods are invertebrates that have similar biological properties to vertebrates such as closed circulation system, an advanced nervous system, and a well-differentiated digestive system. However, it is not currently known whether their microbiomes have more in common with vertebrates or invertebrates. This study reports on the microbial composition of six cephalopod species and compares them with other mollusk and marine fish microbiomes to investigate the factors that shape the gut microbiota. RESULTS: Each cephalopod gut consisted of a distinct consortium of microbes, with Photobacterium and Mycoplasma identified as core taxa. The gut microbial composition of cephalopod reflected their host phylogeny, the importance of which was supported by a detailed oligotype-level analysis of operational taxonomic units assigned to Photobacterium and Mycoplasma. Photobacterium typically inhabited multiple hosts, whereas Mycoplasma tended to show host-specific colonization. Furthermore, we showed that class Cephalopoda has a distinct gut microbial community from those of other mollusk groups or marine fish. We also showed that the gut microbiota of phylum Mollusca was determined by host phylogeny, habitat, and diet. CONCLUSION: We have provided the first comparative analysis of cephalopod and mollusk gut microbial communities. The gut microbial community of cephalopods is composed of distinctive microbes and is strongly associated with their phylogeny. The Photobacterium and Mycoplasma genera are core taxa within the cephalopod gut microbiota. Collectively, our findings provide evidence that cephalopod and mollusk gut microbiomes reflect host phylogeny, habitat, and diet. It is hoped that these data can contribute to future studies on invertebrate-microbe interactions.

Function Analysis of the PR55/B Gene Related to Self-Incompatibility in Chinese Cabbage Using CRISPR/Cas9.

Chinese cabbage, a major crop in Korea, shows self-incompatibility (SI). SI is controlled by the type 2A serine/threonine protein phosphatases (PP2As). The PP2A gene is controlled by regulatory subunits that comprise a 36 kDa catalyst C subunit, a 65 kDa regulatory A subunit, and a variety of regulatory B subunits (50-70 kDa). Among them, the PP2A 55 kDa B regulatory subunit (PR55/B) gene located in the A05 chromosome has 13 exons spanning 2.9 kb, and two homologous genes, Bra018924 and Bra014296, were found to be present on the A06 and A08 chromosome, respectively. In this study, we performed a functional analysis of the PR55/B gene using clustered regularly interspaced short palindromic repeats/CRISPR-associated system 9 (CRISPR/Cas9)-mediated gene mutagenesis. CRISPR/Cas9 technology can be used to easily introduce mutations in the target gene. Tentative gene-edited lines were generated by the Agrobacterium-mediated transfer and were selected by PCR and Southern hybridization analysis. Furthermore, pods were confirmed to be formed in flower pollination (FP) as well as bud pollination (BP) in some gene-edited lines. Seed fertility of gene-edited lines indicated that the PR55/B gene plays a key role in SI. Finally, self-compatible T-DNA-free T2 gene-edited plants and edited sequences of target genes were secured. The self-compatible Chinese cabbage developed in this study is expected to contribute to Chinese cabbage breeding.

Cellulosimicrobium protaetiae sp. nov., isolated from the gut of the larva of Protaetia brevitarsis seulensis.

A Gram-stain-positive, non-spore-forming, yellow-pigmented, non-motile, non-flagellated, facultative anaerobic and rod-shaped bacterial strain, designated BI34T, was isolated from the gut of the larva of Protaetia brevitarsis seulensis. Strain BI34T grew at 15-40 °C (optimum, 37 °C), at pH 6.5-9.0 (optimum, pH 7.5) and in the presence of 0-7 % (w/v) NaCl (optimum, 2 %). Based on the results of 16S rRNA gene sequence analysis, strain BI34T belonged to the phylum Actinobacteria and was closely related to Cellulosimicrobium funkei NBRC 104118T (99.3 %), Cellulosimicrobium cellulans NBRC 15516T (99.1 %), Cellulosimicrobium composti BIT-GX5T (99.0 %), Cellulosimicrobium fucosivorans SE3T (99.0 %), Cellulosimicrobium marinum NBRC 110994T (98.4 %) and Cellulosimicrobium terreum DS-61T (97.0 %). The genome to genome relatedness of the average nucleotide identity (ANI) and the digital DNA-DNA hybridization (dDDH) values calculated by the Genome-to-Genome Distance Calculator between strain BI34T and its related species mentioned above were lower than the threshold of 95 and 70 % for speciation, respectively. The predominant menaquinone of strain BI34T contained MK-9(H4), and the major fatty acids were anteiso-C15 : 0, C16 : 0 and anteiso-C17 : 0. Strain BI34T had diphosphatidylglycerol and phosphatidylglycerol as major polar lipids. The whole-cell sugars were galactose, glucose and ribose, and the cell-wall peptidoglycan contained lysine, alanine, aspartic acid and glutamic acid. The DNA G+C content of strain BI34T was 73.8 mol%. The difference in physiological and biochemical characteristics and the below-threshold values of genome-to-genome relatedness indicate that strain BI34T represents a novel species in the genus Cellulosimicrobium, for which the name Cellulosimicrobium protaetiae sp. nov. is proposed. The type strain is BI34T (=KCTC 49302T=NBRC 114073T).

Halorubrum salinarum sp. nov., an extremely halophilic archaeon isolated from a saturated brine pond of a saltern.

A novel extremely halophilic archaeon, strain RHB-CT, was isolated from a saturated brine pond of a solar saltern in Bolinao, Pangasinan, Philippines. Colonies were orange-red-pigmented, smooth, convex and round on a solid modified growth medium containing 25 % (w/v) of total salts. Cells of strain RHB-CT on the solid modified growth medium were ovoid-shaped (0.89-2.66 µm long), while the cells in a liquid modified growth medium were rod-shaped (1.53-5.65 µm long and 0.45-1.03 µm wide). The strain was Gram-stain-negative, motile and strictly aerobic. Strain RHB-CT grew with NaCl concentrations ranging from 10 to 30 % (w/v; optimum, 20-25 %), at pH 6.5-8.5 (optimum, pH 7.0-7.5) and at 20-55 °C (optimum, 40-45 °C). Furthermore, the strain grew even in the absence of Mg2+; however, when supplemented with Mg2+, growth was observed optimally at 0.2-0.4 M Mg2+. The 16S rRNA gene phylogeny inferred that the strain is a member of the genus Halorubrum and was related to Halorubrum xinjiangense CGMCC 1.3527T (99.0 %), Halorubrum sodomense DSM 3755T (98.8 %), Halorubrum coriense Ch2T (98.8 %), Halorubrum trapanicum NRC 34021T (98.4 %) and Halorubrum distributum JCM 9100T (98.1 %). The rpoB' gene sequences also showed that strain RHB-CT is related to Hrr. xinjiangense JCM 12388T (97.1 %), Hrr. distributum JCM 9100T (97.1 %), Hrr. coriense JCM 9275T (96.5 %), Hrr. californiense JCM 14715T (96.5 %), Hrr. trapanicum JCM 10477T (96.3%), Hrr. sodomense JCM 8880T (96.2%) and Hrr. tebenquichense DSM 14210T (95.6 %). The DNA G+C content of strain RHB-CT was 68.7 mol% (genome). Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain RHB-CT and the closely related species of Halorubrum were below 40 and 90 %, respectively, which are far below the thresholds to delineate a new species. The polar lipids of strain RHB-CT were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulphate and sulfated mannosyl glycosyl diether. Based on dDDH and ANI values, and the significant morphological and physiological differences from known taxa, it is hereby suggested that strain RHB-CT represents a novel species of the genus Halorubrum, for which the name Halorubrum salinarum sp. nov. is proposed. The type strain is RHB-CT (=KCTC 4274T=CMS 2103T).

Anaerostipes hominis sp. nov., a novel butyrate-producing bacteria isolated from faeces of a patient with Crohn's disease.

Cultivation and isolation of gut bacteria are necessary for understanding their role in the intestinal ecosystem. We isolated a novel bacterium, designated strain BG01T, from the faeces of a patient with Crohn's disease. Strain BG01T was a strictly anaerobic, rod-shaped, Gram-variable and endospore-forming bacterium. Strain BG01T possessed C12 : 0, C18 : 0 dimethyl aldehyde (DMA) and C18 : 1 ω9c DMA as predominant cellular fatty acids and meso-diaminopimelic acid as a diagnostic diamino acid. Strain BG01T grew at 15-45 °C (optimum, 37 °C), with 0-4 % (w/v) NaCl (optimum, 0-1 %), at pH 6-10 (optimum, pH 7) and was resistant to bile salt, but not to ampicillin, metronidazole, vancomycin and cefoperazone. Butyrate, propionate, oxalacetate and fumarate were produced as fermentation end products from Gifu anaerobic medium broth. Strain BG01T showed 97.7 % 16S rRNA gene sequence similarity, and 92.0 and 48.5 % of average nucleotide identity and digital DNA-DNA hybridization values, respectively, with Anaerostipes caccae KCTC 15019T. Genomic analysis indicated that strain BG01T had a butyrate-producing pathway. The genomic G+C content of the strain was 43.5 mol%. Results of the phenotypic, phylogenetic and genotypic analyses indicated that strain BG01T represents a novel butyrate-producing species of the genus Anaerostipes, for which the name Anaerostipes hominis sp. nov. is proposed. The type strain is BG01T (=KCTC 15617T=JCM 32275T).

Host habitat is the major determinant of the gut microbiome of fish.

BACKGROUND: Our understanding of the gut microbiota of animals is largely based on studies of mammals. To better understand the evolutionary basis of symbiotic relationships between animal hosts and indigenous microbes, it is necessary to investigate the gut microbiota of non-mammalian vertebrate species. In particular, fish have the highest species diversity among groups of vertebrates, with approximately 33,000 species. In this study, we comprehensively characterized gut bacterial communities in fish. RESULTS: We analyzed 227 individual fish representing 14 orders, 42 families, 79 genera, and 85 species. The fish gut microbiota was dominated by Proteobacteria (51.7%) and Firmicutes (13.5%), different from the dominant taxa reported in terrestrial vertebrates (Firmicutes and Bacteroidetes). The gut microbial community in fish was more strongly shaped by host habitat than by host taxonomy or trophic level. Using a machine learning approach trained on the microbial community composition or predicted functional profiles, we found that the host habitat exhibited the highest classification accuracy. Principal coordinate analysis revealed that the gut bacterial community of fish differs significantly from those of other vertebrate classes (reptiles, birds, and mammals). CONCLUSIONS: Collectively, these data provide a reference for future studies of the gut microbiome of aquatic animals as well as insights into the relationship between fish and their gut bacteria, including the key role of host habitat and the distinct compositions in comparison with those of mammals, reptiles, and birds. Video Abstract.

Pathogenomics of Streptococcus ilei sp. nov., a newly identified pathogen ubiquitous in human microbiome.

Viridans group streptococci are a serious health concern because most of these bacteria cause life-threatening infections, especially in immunocompromised and hospitalized individuals. We focused on two alpha-hemolytic Streptococcus strains (I-G2 and I-P16) newly isolated from an ileostomy effluent of a colorectal cancer patient. We examined their pathogenic potential by investigating their prevalence in human and assessing their pathogenicity in a mouse model. We also predicted their virulence factors and pathogenic features by using comparative genomic analysis and in vitro tests. Using polyphasic and systematic approaches, we identified the isolates as belonging to a novel Streptococcus species and designated it as Streptococcus ilei. Metagenomic survey based on taxonomic assignment of datasets from the Human Microbiome Project revealed that S. ilei is present in most human population and at various body sites but is especially abundant in the oral cavity. Intraperitoneal injection of S. ilei was lethal to otherwise healthy C57BL/6J mice. Pathogenomics and in vitro assays revealed that S. ilei possesses a unique set of virulence factors. In agreement with the in vivo and in vitro data, which indicated that S. ilei strain I-G2 is more pathogenic than strain I-P16, only the former displayed the streptococcal group A antigen. We here newly identified S. ilei sp. nov., and described its prevalence in human, virulence factors, and pathogenicity. This will help to prevent S. ilei strain misidentification in the future, and improve the understanding and management of streptococcal infections.

Calf Diarrhea Caused by Prolonged Expansion of Autochthonous Gut Enterobacteriaceae and Their Lytic Bacteriophages.

Neonatal calf diarrhea is a common disease leading to a major economic loss for cattle producers worldwide. Several infectious and noninfectious factors are implicated in calf diarrhea, but disease control remains problematic because of the multifactorial etiology of the disease. Here, we conducted diagnostic multiplex PCR assay and meta-omics analysis (16S rRNA gene-based metataxonomics and untargeted transcriptional profiling) of rectal content of normal and diarrheic beef calves (n = 111). In the diarrheic calf gut, we detected both microbial compositional dysbiosis (i.e., increased abundances of the family Enterobacteriaceae members and their lytic bacteriophages) and functional dysbiosis (i.e., elevated levels of aerobic respiration and virulence potential). The calf diarrheic transcriptome mirrored the gene expression of the bovine host and was enriched in cellular pathways of sulfur metabolism, innate immunity, and gut motility. We then isolated 12 nontoxigenic Enterobacteriaceae strains from the gut of diarrheic calves. Feeding a strain mixture to preweaning mice resulted in a significantly higher level of fecal moisture content, with decreased body weight gain and shortened colon length. The presented findings suggest that gut inflammation followed by a prolonged expansion of nontoxigenic autochthonous Enterobacteriaceae contributes to the onset of diarrhea in preweaning animals.IMPORTANCE Calf diarrhea is the leading cause of death of neonatal calves worldwide. Several infectious and noninfectious factors are implicated in calf diarrhea, but disease control remains problematic because of the multifactorial etiology of the disease. The major finding of the current study centers around the observation of microbial compositional and functional dysbiosis in rectal samples from diarrheic calves. These results highlight the notion that gut inflammation followed by a prolonged expansion of autochthonous Enterobacteriaceae contributes to the onset of calf diarrhea. Moreover, this condition possibly potentiates the risk of invasion of notorious enteric pathogens, including Salmonella spp., and the emergence of inflammation-resistant (or antibiotic-resistant) microbiota via active horizontal gene transfer mediated by lytic bacteriophages.

Omics in gut microbiome analysis.

Our understanding of the interactions between microbial communities and their niche in the host gut has improved owing to recent advances in environmental microbial genomics. Integration of metagenomic and metataxonomic sequencing data with other omics data to study the gut microbiome has become increasingly common, but downstream analysis after data integration and interpretation of complex omics data remain challenging. Here, we review studies that have explored the gut microbiome signature using omics approaches, including metagenomics, metataxonomics, metatranscriptomics, and metabolomics. We further discuss recent analytics programs to analyze and integrate multi-omics datasets and further utilization of omics data with other advanced techniques, such as adaptive immune receptor repertoire sequencing, microbial culturomics, and machine learning, to evaluate important microbiome characteristics in the gut.

Longitudinal evaluation of fecal microbiota transplantation for ameliorating calf diarrhea and improving growth performance.

Calf diarrhea is associated with enteric infections, and also provokes the overuse of antibiotics. Therefore, proper treatment of diarrhea represents a therapeutic challenge in livestock production and public health concerns. Here, we describe the ability of a fecal microbiota transplantation (FMT), to ameliorate diarrhea and restore gut microbial composition in 57 growing calves. We conduct multi-omics analysis of 450 longitudinally collected fecal samples and find that FMT-induced alterations in the gut microbiota (an increase in the family Porphyromonadaceae) and metabolomic profile (a reduction in fecal amino acid concentration) strongly correlate with the remission of diarrhea. During the continuous follow-up study over 24 months, we find that FMT improves the growth performance of the cattle. This first FMT trial in ruminants suggest that FMT is capable of ameliorating diarrhea in pre-weaning calves with alterations in their gut microbiota, and that FMT may have a potential role in the improvement of growth performance.

ESRRA (estrogen related receptor alpha) is a critical regulator of intestinal homeostasis through activation of autophagic flux via gut microbiota.

The orphan nuclear receptor ESRRA (estrogen related receptor alpha) is critical in mitochondrial biogenesis and macroautophagy/autophagy function; however, the roles of ESRRA in intestinal function remain uncharacterized. Herein we identified that ESRRA acts as a key regulator of intestinal homeostasis by amelioration of colonic inflammation through activation of autophagic flux and control of host gut microbiota. Esrra-deficient mice presented with increased susceptibility to dextran sodium sulfate (DSS)-induced colitis with upregulation of intestinal inflammation. In addition, esrra-null mice had depressed AMP-activated protein kinase phosphorylation (AMPK), lower levels of TFEB (transcription factor EB), and accumulation of SQSTM1/p62 (sequestosome 1) with defective mitochondria in intestinal tissues. Esrra-deficient mice showed distinct gut microbiota composition and significantly higher microbial diversity than wild-type (WT) mice. Cohousing or fecal microbiota transplantation from WT mice to Esrra-deficient mice ameliorated DSS-induced colitis severity. Importantly, patients with ulcerative colitis (UC) had significantly decreased ESRRA expression in intestinal mucosal tissues that correlated with disease activity, suggesting clinical relevance of ESRRA in UC. Taken together, our results show that ESRRA contributes to intestinal homeostasis through autophagy activation and gut microbiota control to protect the host from detrimental inflammation and dysfunctional mitochondria.Abbreviations: ABX, antibotics; AMPK, AMP-activated protein kinase; ATP5A1, ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1; BECN1, beclin1, autophagy related, CCL, C-C motif chemokine ligand; CD, Crohn disease; CLDN, claudin; COX4I1, cytochrome c oxidase subunit 4I1; cKO, conditional knockout; cWT, conditional wild-type; CXCL, C-X-C motif chemokine ligand; DAI, disease activity index; DSS, dextran sodium sulfate; EGFP, enhanced green fluorescent protein; ESRR, estrogen related receptor; ESRRA, estrogen related receptor alpha; Esrra+/+, Esrra wild type; esrra-/-, esrra homozygous knockout; FMT, fecal microbiota transplantation; GABARAP, gamma-aminobutyric acid receptor associated protein; GSEA, gene set enrichment analysis; IBD, inflammatory bowel disease; IL, interleukin; KO, knockout; LAMP1, lysosomal-associated membrane protein 1; LCN2, lipocalin 2; LEfSe, linear discriminant analysis (LDA) effect size; LPS, lipopolysachharide; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; NDUFAB1, NADH: ubiquinone oxidoreductase subunit AB1; OCLN, occludin; OUT, operational taxonomic unit; OXPHOS, oxidative phosphorylation; PCoA, principal coordinate analysis; PPARGC1A, PPARG coactiva- tor 1 alpha; PRKAA, 5'-AMP-activated protein kinase catalytic subunit alpha; PTGS2/COX2, prostaglandin-endoperoxide synthase 2; RAB7, member RAS oncogene family; SDHB, succinate dehydrogenase complex, subunit B, iron sulfur (Ip); SQSTM1/p62, sequestosome 1; S100A9, S100 calcium binding protein A9 (calgranulin B); TCA, tricarboxylic acid; TFEB, transcription factor EB; TNF, tumor necrosis factor; UC, ulcerative colitis; UCP2, uncoupling protein 2 (mitochondrial, proton carrier); UQCRC1, ubiquinol-cytochrome c reductase core protein 1; UVRAG, UV radiation resistance associated gene; Vil1, villin; VPS11, VPS11, CORVET/HOPS core sub-unit; WT, wild type.

Male castration increases adiposity via small intestinal microbial alterations.

Castration of young males is widely used in the cattle industry to improve meat quality, but the mechanism linking hypogonadism and host metabolism is not clear. Here, we use metataxonomic and metabolomic approaches to evaluate the intestinal microbiota and host metabolism in male, castrated male (CtM), and female cattle. After pubescence, the CtM cattle harbor distinct ileal microbiota dominated by the family Peptostreptococcaceae and exhibit distinct serum and muscle amino acid profiles (i.e., highly abundant branched-chain amino acids), with increased extra- and intramuscular fat storage. We also evaluate the causative factor(s) that underpin the alteration of the intestinal microbiota and host metabolic phenotype in response to hypogonadism. Castration of male mice phenocopies both the intestinal microbial alterations and obese-prone metabolism observed in cattle. Antibiotic treatment and fecal microbiota transplantation experiments in a mouse model confirm that the intestinal microbial alterations associated with hypogonadism are a key contributor to the obese phenotype in the CtM animals. Collectively, targeting the gut microbiota is a potential therapeutic strategy for the treatment of both hypogonadism and obesity.

First identification of Anaplasma phagocytophilum in both a biting tick Ixodes nipponensis and a patient in Korea: a case report.

BACKGROUND: Human granulocytic anaplasmosis (HGA) is a tick-borne infectious disease caused by Anaplasma phagocytophilum. To date, there have been no reported cases of A. phagocytophilum infection found in both the biting tick and the patient following a tick bite. CASE PRESENTATION: An 81-year-old woman presented with fever following a tick bite, with the tick still intact on her body. The patient was diagnosed with HGA. The tick was identified as Ixodes nipponensis by morphological and molecular biological detection methods targeting the 16S rRNA gene. The patient's blood was cultured after inoculation into the human promyelocytic leukemia cell line HL-60. A. phagocytophilum growth was confirmed via culture and isolation. A. phagocytophilum was identified in both the tick and the patient's blood by Anaplasma-specific groEL- and ankA-based nested polymerase chain reaction followed by sequencing. Moreover, a four-fold elevation in antibodies was observed in the patient's blood. CONCLUSION: We report a case of a patient diagnosed with HGA following admission for fever due to a tick bite. A. phagocytophilum was identified in both the tick and the patient, and A. phagocytophilum was successfully cultured. The present study suggests the need to investigate the possible incrimination of I. nipponensis as a vector for HGA in Korea.

Flaviflexus ciconiae sp. nov., isolated from the faeces of the oriental stork, Ciconia boyciana.

A novel Gram-stain-positive, non-motile, non-spore-forming, coccobacillus-shaped, strictly aerobic bacterium, designated strain H23T48T, was isolated from the faecal sample of an oriental stork collected from the Seoul Grand Park Zoo in Seoul, Republic of Korea. Optimal growth of strain H23T48T was observed at 30-37 °C, pH 8 and with 3 % (w/v) NaCl. 16S rRNA gene sequence-based phylogenetic analysis revealed that strain H23T48T was closely related to the genus Flaviflexus, with 97.0 and 96.7 % sequence similarities to Flaviflexus salsibiostraticola EBR4-1-2T and Flaviflexus huanghaiensis H5T, respectively. Strain H23T48T possessed MK-9(H4) as the major menaquinone and C16 : 0 (42.4 %), C18 : 1 ω9c (31.3 %) and C14 : 0 (17.7 %) as the major cellular fatty acids. The polar lipids included phosphatidylglycerol, two unidentified lipids, six unidentified phospholipids and two unidentified glycophospholipids. The amino acid composition of the cell-wall peptidoglycan was l-alanine, l-lysine, d-glutamic acid, l-aspartic acid and glycine. The genomic G+C content of strain H23T48T is 59.5 mol% and the average nucleotide identity value between H23T48T and F. salsibiostraticola KCT C33148T (=EBR4-1-2T) is 75.5 %. Based on the obtained data, strain H23T48T represents a novel species of the genus Flaviflexus, for which the name Flaviflexus ciconiae sp. nov. is proposed. The type strain is H23T48T (=KCTC 49253T=JCM 33282T).

Jeotgalibaca ciconiae sp. nov., isolated from the faeces of an Oriental stork.

A novel, Gram-stain-positive, non-spore-forming, facultatively anaerobic bacterium, designated strain H21T32T, was isolated from the faeces of an Oriental stork, Ciconia boyciana. Cells formed cocci grouped in pairs, tetrads or conglomerates, and colonies on solid medium were pale yellow. Strain H21T32T belonged to the genus Jeotgalibaca, family Carnobacteriaceae, order Lactobacillales and class Bacilli. The 16S rRNA gene sequences of the strain showed 97.06-97.34, 96.17-96.31 and 95.93-96.07 % similarity to the type strains of Jeotgalibaca arthritidis, J. porci and J. dankookensis, respectively. The strain grew at 10-37 °C (optimum temperature: 30 °C), with 0-7 % (w/v) NaCl (optimum salinity: 0.5 %) and at pH 7-9 (optimum pH: 8). The main cellular fatty acids were C16 : 1 ω9c, C18 : 1 ω9c and C16 : 0. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. Respiratory quinones were not detected. Sugar components of the peptidoglycan were rhamnose, ribose and glucose. Amino acid components of the cell wall were l-alanine, d-glucose, l-lysine, glycine and aspartic acid. The DNA G+C content of the strain was 37.1 mol%. Average nucleotide identity between strain H21T32T and J. arthritidis CECT 9157T was 77.02 %, confirming that strain H21T32T represents a novel species of the genus Jeotgalibaca, for which the name Jeotgalibaca ciconiae sp. nov. is proposed. The type strain is H21T32T (=KCTC 33991T=JCM 33222T).

Haloplanus rubicundus sp. nov., an extremely halophilic archaeon isolated from solar salt.

Two extremely halophilic archaea strains, CBA1112T and CBA1113, were isolated from solar salt in Korea. The genome sizes and G+C content of CBA1112T and CBA1113 were 3.77 and 3.53Mb, and 66.0 and 66.5mol%, respectively. Phylogenetic analysis based on closely related taxa and environmental Haloplanus sequences indicated that both CBA1112T and CBA1113 strains are grouped within the genus Haloplanus. OrthoANI and in silico DNA-DNA hybridization values were below the species delineation threshold. Pan-genomic analysis showed that the two novel strains and four reference strains had 6203 pan-orthologous groups in total. Six Haloplanus strains shared 1728 core pan-genome orthologous groups, which were mainly associated with amino acid transport and metabolism and translation, ribosomal structure and biogenesis categories, and amino acid metabolism and carbohydrate metabolism related categories. The novel strain-specific pan-genome orthologous groups were mainly involved with replication, recombination and repair category and replication and repair pathway or amino acid metabolism pathway. Cells of both strains were Gram-negative and pleomorphic, and colonies were red-pigmented. The major polar lipids of both strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, and one glycolipid, sulfated mannosyl glucosyl diether. Based on genomic, phylogenetic, phenotypic, and chemotaxonomic features, strains CBA1112T and CBA1113 are described as novel species of the genus Haloplanus. Thus, we propose the name Haloplanus rubicundus sp. nov. The type strain is CBA1112T (=KCCM 43224T=JCM 30475T).