Ji-Hyun Yun

Insect gut bacterial diversity determined by environmental habitat, diet, developmental stage, and phylogeny of host.

ABSTRACT Insects are the most abundant animals on Earth, and the microbiota within their guts play important roles by engaging in beneficial and pathological interactions with these hosts. In this study, we comprehensively characterized insect-associated gut bacteria of 305 individuals belonging to 218 species in 21 taxonomic orders, using 454 pyrosequencing of 16S rRNA genes. In total, 174,374 sequence reads were obtained, identifying 9,301 bacterial operational taxonomic units (OTUs) at the 3% distance level from all samples, with an average of 84.3 (±97.7) OTUs per sample. The insect gut microbiota were dominated by Proteobacteria (62.1% of the total reads, including 14.1% Wolbachia sequences) and Firmicutes (20.7%). Significant differences were found in the relative abundances of anaerobes in insects and were classified according to the criteria of host environmental habitat, diet, developmental stage, and phylogeny. Gut bacterial diversity was significantly higher in omnivorous insects than in stenophagous (carnivorous and herbivorous) insects. This insect-order-spanning investigation of the gut microbiota provides insights into the relationships between insects and their gut bacterial communities.

Chronic Repression of mTOR Complex 2 Induces Changes in the Gut Microbiota of Diet-induced Obese Mice

Alterations in the gut microbiota play a crucial role in host physiology and metabolism; however, the molecular pathways underlying these changes in diet-induced obesity are unclear. Mechanistic target of rapamycin (mTOR) signaling pathway is associated with metabolic disorders such as obesity and type 2 diabetes (T2D). Therefore, we examined whether changes in the regulation of mTOR signaling induced by diet (a high-fat diet [HFD] or normal-chow diet) and/or therapeutics (resveratrol [a specific inhibitor of mTOR complex 1] or rapamycin [an inhibitor of both mTOR complex 1 and 2]) altered the composition of the gut microbiota in mice. Oral administration of resveratrol prevented glucose intolerance and fat accumulation in HFD-fed mice, whereas rapamycin significantly impaired glucose tolerance and exacerbated intestinal inflammation. The abundance of Lactococcus, Clostridium XI, Oscillibacter, and Hydrogenoanaerobacterium increased under the HFD condition; however, the abundance of these species declined after resveratrol treatment. Conversely, the abundance of unclassified Marinilabiliaceae and Turicibacter decreased in response to a HFD or rapamycin. Taken together, these results demonstrated that changes in the composition of intestinal microbiota induced by changes in mTOR activity correlate with obese and diabetic phenotypes.

Kocuria salsicia sp. nov., isolated from salt-fermented seafood

Strain 104(T) was isolated from a traditional salt-fermented seafood in Korea. It was a Gram-positive, non-motile, coccus-shaped bacterium. It formed lemon-yellow, opaque colonies that were circular with entire margins. Optimal growth occurred at 30-37 °C, pH 7-8 and in the presence of 0-2 % (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene sequences from strain 104(T) and reference species of the genus Kocuria indicated that strain 104(T) formed an independent line. The G+C content of the chromosomal DNA was 60.6 mol%. MK-7 was the major menaquinone and the predominant fatty acids were anteiso-C(15 : 0) (76.7 %), anteiso-C(17 : 0) (10.9 %) and iso-C(16 : 0) (4.5 %). Strain 104(T) was most closely related to Kocuria rhizophila TA68(T) (98.9 % 16S rRNA gene sequence similarity). The DNA-DNA hybridization value between strain 104(T) and K. rhizophila TA68(T) was 14.1±3.4 %. On the basis of this polyphasic taxonomic analysis, strain 104(T) appears to represent a novel species in the genus Kocuria. The name Kocuria salsicia sp. nov. is proposed. The type strain is 104(T) (=KACC 21128(T)=JCM 16361(T)).

Leucobacter salsicius sp. nov., from a salt- fermented food

Strain M1-8(T) was isolated from jeotgal, a Korean salt-fermented food. Cells were aerobic, non-motile, Gram-reaction-positive and rod-shaped. Colonies were cream-coloured and circular with entire margins. Strain M1-8(T) exhibited optimal growth at 25-30 °C and pH 7.0-8.0 and in 0-4  % (w/v) NaCl. The strain tolerated up to 10.0 mM Cr(VI). Phylogenetic analyses of 16S rRNA gene sequences indicated that strain M1-8(T) represents a novel species in the genus Leucobacter. The 16S rRNA gene sequence of M1-8(T) exhibited 98.1  % similarity to that of Leucobacter chromiireducens subsp. chromiireducens L-1(T). The new isolate was clustered with Leucobacter species on a 16S rRNA gene sequence-based phylogenetic tree. The chromosomal DNA G+C content of strain M1-8(T) was 62.8 %. Its cell-wall peptidoglycan contained 2,4-diaminobutyric acid, glutamic acid, alanine, glycine and γ-aminobutyric acid. The major menaquinone was MK-11 and the predominant fatty acids were anteiso-C₁₅:₀ (63.6 %), anteiso-C₁₇:₀ (16.7 %) and iso-C₁₆:₀ (14.2  %). The polar lipid profile of strain M1-8(T) contained diphosphatidylglycerol and one unknown glycolipid. Significant genotypic and phenotypic differences were found between strain M1-8(T) and other Leucobacter species. These differentiating characteristics indicate that strain M1-8(T) represents a novel species of the genus Leucobacter, for which the name Leucobacter salsicius sp. nov. is proposed. The type strain is M1-8(T) (=KACC 21127(T) =JCM 16362(T)).

Blastopirellula cremea sp. nov., isolated from a dead ark clam.

Strain LHWP2(T), a novel, aerobic, budding, motile and ovoid bacterium belonging to the phylum Planctomycetes, was isolated from a dead ark clam (Scapharca broughtonii) from the south coast of Korea. Strain LHWP2(T) grew optimally at 30 °C, in the presence of 4% (w/v) NaCl, and at pH 7. The predominant cellular fatty acids were C16:0, C18:1ω7c and/or C18:1ω6c (summed feature 8) and C18:1ω9c. The major isoprenoid quinone was menaquinone-6 (MK-6). The dominant polar lipid was identified as phosphatidylglycerol. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel strain was most closely related to Blastopirellula marina DSM 3645(T), with a 16S rRNA gene sequence similarity of 94.1%. The genomic DNA G+C content of strain LHWP2(T) was 49.5 mol%. Strain LHWP2(T) was distinguished from B. marina DSM 3645(T) based on its optimum salinity, acid production from substrates, assimilation of substrates and DNA G+C content. Overall, these phenotypic, genotypic and phylogenetic data suggest that strain LHWP2(T) should be classified as a novel species belonging to the genus Blastopirellula, for which the name Blastopirellula cremea sp. nov. is proposed. The type strain is LHWP2(T) (=KACC 15559(T)=JCM 17758(T)).

Acinetobacter apis sp. nov., isolated from the intestinal tract of a honey bee, Apis mellifera

A novel Gram-negative, obligate aerobic, non-motile, and both coccobacillus- and bacillus-shaped bacterium, designated strain HYN18T, was isolated from the intestinal tract of a honey bee (Apis mellifera). The isolate was oxidasenegative and catalase-positive. Strain HYN18T showed optimum growth at 25°C, pH 6–7, and in the presence of 1% (w/v) NaCl in trypticase soy broth medium. The isolate was negative for hydrolyses of starch, casein, gelatin and urea, indole production from tryptone and hemolysis on sheep blood agar. A phylogenetic analysis based on the 16S rRNA gene and rpoB gene sequence showed that strain HYN18T was most closely related to Acinetobacter nectaris SAP 763.2T and A. boissieri SAP 284.1T with 98.3% and 98.1% similarity (16S rRNA gene), respectively, and 84.4% similarity with Acinetobacter nectaris SAP 763.2T (rpoB gene). The major cellular fatty acids were summed features 3 (comprising C16:1ω7c/C16:1ω6c), C12:0 and C16:0. The main isoprenoid quinone was ubiquinone-9 (Q-9). The polar lipids of strain HYN18T were phosphatidylethanolamine, three unidentified lipids, an unidentified phospholipid and an unidentified glycolipid. The DNA G+C content was 40.6 mol%. DNADNA hybridization experiments indicated less than 33 ± 10% relatedness to the closest phylogenetic species, Acinetobacter nectaris SAP 763.2T. Thus, the phenotypic, phylogenetic and genotypic analyses indicate that strain HYN18T is a novel species within the genus Acinetobacter, for which the name Acinetobacter apis is proposed. The type strain is HYN18T (=KACC 16906T =JCM 18575T).

Orbus sasakiae sp. nov., a bacterium isolated from the gut of the butterfly Sasakia charonda, and emended description of the genus Orbus

A novel Gram-stain-negative, facultatively anaerobic, non-motile and coccus-shaped bacterium, strain C7(T), was isolated from the gut of the butterfly Sasakia charonda. Strain C7(T) grew optimally at 20-25 °C, at pH 7-8 and with 1 % (w/v) NaCl. The strain was negative for oxidase activity but positive for catalase activity. The 16S rRNA gene sequences of strain C7(T) and Orbus hercynius CN3(T) shared 96.8 % similarity. The major fatty acids identified were C14 : 0, C16 : 0, C18 : 1ω7c and summed feature 2 (comprising C14 : 0 3-OH/iso-C16 : 1). The major respiratory quinone was ubiquinone-8 (Q-8). The polar lipids of strain C7(T) were phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid and two unidentified aminophospholipids. The G+C content of the genomic DNA extracted from strain C7(T) was 32.1 mol%. Taken together, the phenotypic, genotypic and phylogenetic analyses indicate that strain C7(T) represents a novel species of the genus Orbus, for which the name Orbus sasakiae sp. nov. is proposed. The type strain is C7(T) ( = KACC 16544(T) = JCM 18050(T)). An emended description of the genus Orbus is provided.

Weissella diestrammenae sp. nov., isolated from the gut of a camel cricket (Diestrammena coreana)

A novel, Gram-stain-positive, non-motile, facultatively anaerobic, rod- or coccoid-shaped bacterium, designated strain ORY33(T), was isolated from the gut of a camel cricket (Diestrammena coreana). The 16S rRNA gene sequence analysis showed that strain ORY33(T) belonged to the genus Weissella, with highest sequence similarity to Weissella koreensis S-5623(T) (97.7 %). The strain grew optimally at 30 °C and pH 7 in the presence of 0 % (w/v) NaCl. Catalase and oxidase activities were negative. The genomic DNA G+C content of strain ORY33(T) was 45.1 mol%. DNA-DNA hybridization values between strain ORY33(T) and closely related members of the genus Weissella were less than 27 %. The major fatty acids of strain ORY33(T) were C18 : 1ω9c, C16 : 0 and C14 : 0. Based on these phenotypic, phylogenetic and genotypic analyses, strain ORY33(T) represents a novel species belonging to the genus Weissella, for which the name Weissella diestrammenae sp. nov. is proposed. The type strain is ORY33(T) (= KACC 16890(T) = JCM 18559(T)).

Gibbsiella papilionis sp. nov., isolated from the intestinal tract of the butterfly Mycalesis gotama, and emended description of the genus Gibbsiella

A novel Gram-negative, non-motile, facultative anaerobic and rod-shaped bacterium, designated strain LEN33(T), was isolated from the intestinal tract of a butterfly (Mycalesis gotama). Strain LEN33(T) grew optimally at 37 °C in the presence of 1 % (w/v) NaCl and at pH 9. The novel strain was oxidase-negative and catalase-positive. The major cellular fatty acids were C14 : 0, C16 : 0 and cyclo-C17 : 0. Strain LEN33(T) contained two unidentified lipids, three unidentified amino-phospholipids, phosphatidylethanolamine (PE) and phosphatidylglycerol (PG). The major isoprenoid quinone was ubiquinone-8 (Q-8). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain LEN33(T) was most closely related to Gibbsiella quercinecans FRB 97(T) and Gibbsiella dentisursi NUM 1720(T), with 98.7 % similarities. DNA-DNA hybridization experiments indicated less than 40.7 ± 2 % relatedness to the closest phylogenetic species, G. quercinecans FRB 97(T). The G+C content of genomic DNA was 58.7 mol%. Phenotypic, phylogenetic and genotypic analysis indicated that strain LEN33(T) represents a novel species within the genus Gibbsiella, for which the name Gibbsiella papilionis is proposed. The type strain is referred to as LEN33(T) ( = KACC 16707(T) = JCM 18389(T)). An emended description of the genus Gibbsiella is also proposed.

Genome sequence of the chromate-resistant bacterium Leucobacter salsicius type strain M1-8(T.).

Leucobacter salsicius M1-8T is a member of the Microbacteriaceae family within the class Actinomycetales. This strain is a Gram-positive, rod-shaped bacterium and was previously isolated from a Korean fermented food. Most members of the genus Leucobacter are chromate-resistant and this feature could be exploited in biotechnological applications. However, the genus Leucobacter is poorly characterized at the genome level, despite its potential importance. Thus, the present study determined the features of Leucobacter salsicius M1-8T, as well as its genome sequence and annotation. The genome comprised 3,185,418 bp with a G+C content of 64.5%, which included 2,865 protein-coding genes and 68 RNA genes. This strain possessed two predicted genes associated with chromate resistance, which might facilitate its growth in heavy metal-rich environments.