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Journal Article
- Lysobacter arenosi sp. nov. and Lysobacter solisilvae sp. nov. isolated from soil
- Kyeong Ryeol Kim† , Kyung Hyun Kim† , Shehzad Abid Khan , Hyung Min Kim , Dong Min Han , Che Ok Jeon
- J. Microbiol. 2021;59(8):709-718. Published online June 1, 2021
- DOI: https://doi.org/10.1007/s12275-021-1156-y
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- 8 Citations
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Abstract
- Two Gram-stain negative, yellow-pigmented, and mesophilic bacteria, designated strains R7T and R19T, were isolated from sandy and forest soil, South Korea, respectively. Both strains were non-motile rods showing catalase- and oxidase-positive activities. Both strains were shown to grow at 10–37°C and pH 6.0–9.0, and in the presence of 0–1.5% (w/v) NaCl. Strain R7T contained iso-C14:0, iso-C15:0, iso-C16:0, and summed feature 9 (comprising C16:0 10-methyl and/or iso-C17:1 ω9c), whereas strain R19T contained iso-C11:0 3-OH, C16:1 ω7c alcohol, iso-C11:0, iso-C15:0, iso-C16:0, and summed feature 9 (comprising C16:0 10-methyl and/or iso-C17:1 ω9c) as major cellular fatty acids (> 5%). Both strains contained ubiquinone- 8 as the sole isoprenoid quinone and phosphatidylglycerol, phosphatidylethanolamine, and an unidentified phospholipid as the major polar lipids. The DNA G + C contents of strains R7T and R19T calculated from their genomes were 66.9 mol% and 68.9 mol%, respectively. Strains R7T and R19T were most closely related to Lysobacter panacisoli C8-1T and Lysobacter niabensis GH34-4T with 98.7% and 97.8% 16S rRNA sequence similarities, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains R7T and R19T formed distinct phylogenetic lineages within the genus Lysobacter. Based on phenotypic, chemotaxonomic, and molecular features, strains R7T and R19T represent novel species of the genus Lysobacter, for which the names Lysobacter arenosi sp. nov. and Lysobacter solisilvae sp. nov. are proposed. The type strains of L. arenosi and L. solisilvae are R7T (= KACC 21663T = JCM 34257T) and R19T (= KACC 21767T = JCM 34258T), respectively.
Review
- Omics in gut microbiome analysis
- Tae Woong Whon , Na-Ri Shin , Joon Yong Kim , Seong Woon Roh
- J. Microbiol. 2021;59(3):292-297. Published online February 23, 2021
- DOI: https://doi.org/10.1007/s12275-021-1004-0
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- 39 Citations
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Abstract
- 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.
Journal Article
- Impact of feeding regimens on the composition of gut microbiota and metabolite profiles of plasma and feces from Mongolian sheep
- Bohui Wang , Yulong Luo , Rina Su , Duo Yao , Yanru Hou , Chang Liu , Rui Du , Ye Jin
- J. Microbiol. 2020;58(6):472-482. Published online April 22, 2020
- DOI: https://doi.org/10.1007/s12275-020-9501-0
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- 20 Citations
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Abstract
- Mongolian sheep are an indigenous ruminant raised for wool and meat production in China. The gut microbial community plays an important role in animal performance and metabolism. The objective of this study was to investigate the effects of two feeding regimens on the diversity and composition of gut microbiota and metabolite profiles of feces and plasma from Mongolian sheep. A total of 20 Mongolian sheep were assigned to one of two feeding regimens: free grazing (FG) and barn confinement (BC). When samples were collected, the average live weights of the sheep were 31.28 ± 1.56 kg and 34.18 ± 1.87 kg for the FG and BC groups, respectively. At the genus level, the FG group showed higher levels of Bacteroides, RC9_gut_group, Alistipes, Phocaeicola, Barnesiella, and Oscillibacter, and lower levels of Succinivibrio, Treponema, and Prevotella, compared to the BC group. The butyric acid content in feces was lower in the FG group (P < 0.05). Higher levels of palmitic acid, oleic acid, alpha-linolenic acid, L-carnitine, L-citrulline, and L-histidine, and lower levels of L-tyrosine, L-phenylalanine, and L-kynurenine were found in the plasma of the FG sheep. Moreover, there were substantial associations between several gut microbiota genera and alterations in feces and plasma metabolites especially those involved in the metabolism of butyric acid, linolenic acid, and L-tyrosine. Feeding regimens can not only influence the composition of gut microbiota, but also alter metabolic homeostasis in sheep.
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