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Jo H, Han G, Kim EB, Kong C, Kim BG. Effects of supplemental bacteriophage on the gut microbiota and nutrient digestibility of ileal-cannulated pigs. J Anim Sci Technol 2024; 66:340-352. [PMID: 38628684 PMCID: PMC11016748 DOI: 10.5187/jast.2023.e96] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/02/2023] [Accepted: 09/10/2023] [Indexed: 04/19/2024]
Abstract
This study measured the potential changes of the microbiota in the gastrointestinal tract and energy and nutrient digestibility by supplemental bacteriophages in pigs. Twelve castrated male pigs (initial mean body weight = 29.5 ± 2.3 kg) were surgically cannulated using T-cannula. The animals were housed individually in pens equipped with a feeder and a nipple waterer. The pigs were allotted to 1 of 3 experimental diets in a quadruplicated 3 × 2 Latin square design with 3 experimental diets, 2 periods, and 12 pigs resulting in 8 replicates per diet. The 3 diets were a control mainly based on corn and soybean meal with no antibiotics or bacteriophages, a diet containing 0.1% antibiotics, and a diet containing 0.2% bacteriophages. On day 5 of the experimental period, feces were collected and on days 6 and 7, ileal digesta were collected. Genomic DNA for bacteria were extracted from the ileal digesta and feces and the V4 region of the 16S rRNA gene was amplified. The ileal and fecal digestibility of energy, dry matter, organic matter, crude protein, and fiber was unaffected by dietary antibiotics or bacteriophages. At the phylum level, the supplemental antibiotic or bacteriophage tended to result in a higher proportion of Firmicutes (p = 0.059) and a lower proportion of Bacteroidetes (p = 0.099) in the ileal digesta samples compared with the control group with no difference between the antibiotic and bacteriophage groups. At the genus level, the supplemental antibiotic or bacteriophage tended to result in a higher proportion of Lactobacillus (p = 0.062) and a lower proportion of Bacteroides (p = 0.074) and Streptococcus (p = 0.088) in the ileal digesta compared with the control group with no difference between the antibiotic and bacteriophage groups. In the feces, supplemental antibiotics or bacteriophages reduced the proportion of Bifidobacterium compared with the control group (p = 0.029) with no difference between the antibiotic and bacteriophage groups. Overall, supplemental antibiotics and bacteriophages showed positive effect on the microbiota of in the ileal digesta without largely affecting energy or nutrient digestibility, with no differences between the antibiotic and bacteriophage groups in growing pigs.
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Affiliation(s)
- Hyunwoong Jo
- Monogastric Animal Feed Research
Institute, Konkuk University, Seoul 05029, Korea
| | - Geongoo Han
- Molecular Microbiology and Immunology,
Brown University, Providence 02912, Rhode Island, USA
| | - Eun Bae Kim
- Department of Applied Animal Science,
Kangwon National University, Chuncheon 24341, Korea
| | - Changsu Kong
- Department of Animal Science, Kyungpook
National University, Sangju 37224, Korea
| | - Beob Gyun Kim
- Monogastric Animal Feed Research
Institute, Konkuk University, Seoul 05029, Korea
- Department of Animal Science and
Technology, Konkuk University, Seoul 05029, Korea
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2
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Choi S, Kim EB. A comprehensive longitudinal study of gut microbiota dynamic changes in laying hens at four growth stages prior to egg production. Anim Biosci 2023; 36:1727-1737. [PMID: 37871901 PMCID: PMC10623045 DOI: 10.5713/ab.23.0271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/14/2023] [Accepted: 10/16/2023] [Indexed: 10/25/2023] Open
Abstract
OBJECTIVE The poultry industry is a primary source of animal protein worldwide. The gut microbiota of poultry birds, such as chickens and ducks, is critical in maintaining their health, growth, and productivity. This study aimed to identify longitudinal changes in the gut microbiota of laying hens from birth to the pre-laying stage. METHODS From a total of 80 Hy-Line Brown laying hens, birds were selected based on weight at equal intervals to collect feces (n = 20 per growth) and ileal contents (n = 10 per growth) for each growth stage (days 10, 21, 58, and 101). The V4 regions of the 16S rRNA gene were amplified after extracting DNA from feces and ileal contents. Amplicon sequencing was performed using Illumina, followed by analysis. RESULTS Microbial diversity increased with growth stages, regardless of sampling sites. Microbial community analysis indicated that Firmicutes, Proteobacteria, and Bacteroidetes were the dominant phyla in the feces and ileal. The abundance of Lactobacillus was highest on day 10, and that of Escherichia-shigella was higher on day 21 than those at the other stages at the genus level (for the feces and ileal contents; p<0.05). Furthermore, Turicibacter was the most abundant genus after changing feed (for the feces and ileal contents; p<0.05). The fecal Ruminococcus torques and ileal Lysinibacillus were negatively correlated with the body weights of chickens (p<0.05). CONCLUSION The gut microbiota of laying hens changes during the four growth stages, and interactions between microbiota and feed may be present. Our findings provide valuable data for understanding the gut microbiota of laying hens at various growth stages and future applied studies.
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Affiliation(s)
- Seojin Choi
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, 24341,
Korea
| | - Eun Bae Kim
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, 24341,
Korea
- Institute of Animal Life Science, Kangwon National University, Chuncheon, 24341,
Korea
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3
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Xuan B, Park J, Lee GS, Kim EB. Oral Administration of Mice with Cell Extracts of Recombinant
Lactococcus lactis IL1403 Expressing Mouse
RANKL. Food Sci Anim Resour 2022; 42:1061-1073. [DOI: 10.5851/kosfa.2022.e54] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/08/2022] [Accepted: 09/05/2022] [Indexed: 11/06/2022] Open
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Yu AO, Goldman EA, Brooks JT, Golomb BL, Yim IS, Gotcheva V, Angelov A, Kim EB, Marco ML. Strain diversity of plant-associated Lactiplantibacillus plantarum. Microb Biotechnol 2021; 14:1990-2008. [PMID: 34171185 PMCID: PMC8449665 DOI: 10.1111/1751-7915.13871] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 06/04/2021] [Accepted: 06/06/2021] [Indexed: 01/05/2023] Open
Abstract
Lactiplantibacillus plantarum (formerly Lactobacillus plantarum) is a lactic acid bacteria species found on plants that is essential for many plant food fermentations. In this study, we investigated the intraspecific phenotypic and genetic diversity of 13 L. plantarum strains isolated from different plant foods, including fermented olives and tomatoes, cactus fruit, teff injera, wheat boza and wheat sourdough starter. We found that strains from the same or similar plant food types frequently exhibited similar carbohydrate metabolism and stress tolerance responses. The isolates from acidic, brine‐containing ferments (olives and tomatoes) were more resistant to MRS adjusted to pH 3.5 or containing 4% w/v NaCl, than those recovered from grain fermentations. Strains from fermented olives grew robustly on raffinose as the sole carbon source and were better able to grow in the presence of ethanol (8% v/v or sequential exposure of 8% (v/v) and then 12% (v/v) ethanol) than most isolates from other plant types and the reference strain NCIMB8826R. Cell free culture supernatants from the olive‐associated strains were also more effective at inhibiting growth of an olive spoilage strain of Saccharomyces cerevisiae. Multi‐locus sequence typing and comparative genomics indicated that isolates from the same source tended to be genetically related. However, despite these similarities, other traits were highly variable between strains from the same plant source, including the capacity for biofilm formation and survival at pH 2 or 50°C. Genomic comparisons were unable to resolve strain differences, with the exception of the most phenotypically impaired and robust isolates, highlighting the importance of utilizing phenotypic studies to investigate differences between strains of L. plantarum. The findings show that L. plantarum is adapted for growth on specific plants or plant food types, but that intraspecific variation may be important for ecological fitness and strain coexistence within individual habitats.
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Affiliation(s)
- Annabelle O Yu
- Department of Food Science and Technology, University of California, Davis, Davis, CA, USA
| | - Elissa A Goldman
- Department of Food Science and Technology, University of California, Davis, Davis, CA, USA
| | - Jason T Brooks
- Department of Food Science and Technology, University of California, Davis, Davis, CA, USA
| | - Benjamin L Golomb
- Department of Food Science and Technology, University of California, Davis, Davis, CA, USA
| | - Irene S Yim
- Department of Food Science and Technology, University of California, Davis, Davis, CA, USA
| | - Velitchka Gotcheva
- Department of Biotechnology, University of Food Technologies, Plovdiv, Bulgaria
| | - Angel Angelov
- Department of Biotechnology, University of Food Technologies, Plovdiv, Bulgaria
| | - Eun Bae Kim
- Department of Applied Animal Science, Kangwon National University, Chuncheon, Gangwon-Do, South Korea
| | - Maria L Marco
- Department of Food Science and Technology, University of California, Davis, Davis, CA, USA
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Oh SH, Kim SH, Jeon JH, Kim EB, Lee NK, Beck S, Choi YJ, Kang SK. Cytoplasmic expression of a model antigen with M Cell-Targeting moiety in lactic acid bacteria and implication of the mechanism as a mucosal vaccine via oral route. Vaccine 2021; 39:4072-4081. [PMID: 34127296 DOI: 10.1016/j.vaccine.2021.06.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 05/27/2021] [Accepted: 06/03/2021] [Indexed: 11/15/2022]
Abstract
Lactic acid bacteria (LAB) have been widely studied as mucosal vaccine delivery carriers against many infectious diseases for heterologous expression of protein antigens. There are three antigen expression strategies for LAB: cytoplasmic expression (CE), cell surface display (SD), and extracellular secretion (ES). Despite the generally higher protein expression level and many observations of antigen-specific immunogenicity in CE, its application as a mucosal vaccine has been overlooked relative to SD and ES because of the antigens enclosed by the LAB cell wall. We hypothesized that the antigens in CE could be released from the LAB into the intestinal lumen before host bacterial access to gut-associated lymphoid tissue (GALT), which could contribute to antigen-specific immune responses after oral administration. To elucidate this hypothesis, three recombinant Lactobacillus plantarum (LP) strains were constructed to produce a model antigen, BmpB, with or without an M cell-targeting moiety, and their immunogenicities were analyzed comparatively as oral vaccines in mouse model. The data indicated that the recombinant LPs producing BmpBs with different conformations could induce mucosal immunity differentially. This suggests that the cytoplasmic antigens in LAB could be released into the intestinal lumen, subsequently translocated through M cells, and stimulate the GALT to generate antigen-specific immune responses. Therefore, the CE strategy has great potential, especially in the application of oral LAB vaccines as well as SD and ES strategies. This research provides a better understanding of the mechanism for recombinant oral LAB vaccines and gives insight to the future design of LAB vaccines and oral delivery applications for useful therapeutic proteins.
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Affiliation(s)
- Seo-Ho Oh
- Institute of Green-Bio Science & Technology, Seoul National University, Pyeongchang-gun 25354, Republic of Korea
| | - Sung-Hee Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea; Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Ji-Hye Jeon
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea; Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Eun Bae Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea; Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Nam-Kyung Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea; Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Samuel Beck
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea; Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Yun-Jaie Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea; Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang-Kee Kang
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang-gun 25354, Republic of Korea; Institute of Green-Bio Science & Technology, Seoul National University, Pyeongchang-gun 25354, Republic of Korea; Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Republic of Korea.
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Xuan B, Park J, Choi S, You I, Nam BH, Noh ES, Kim EM, Song MY, Shin Y, Jeon JH, Kim EB. Draft Genome of the Korean smelt Hypomesus nipponensis and its transcriptomic responses to heat stress in the liver and muscle. G3 (Bethesda) 2021; 11:6263857. [PMID: 33944944 PMCID: PMC8496316 DOI: 10.1093/g3journal/jkab147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 04/23/2021] [Indexed: 12/13/2022]
Abstract
Pond smelt (Hypomesus nipponensis) is a cold-freshwater fish species and a winter economic aquaculture resource in South Korea. Because of its high susceptibility to abnormal water temperature from global warming, a large number of smelt die in hot summers. Here, we present the first draft genome of H. nipponensis and transcriptomic changes in molecular mechanisms or intracellular responses under heat stress. We combined Illumina and PacBio sequencing technologies to generate the draft genome of H. nipponensis. Based on the reference genome, we conducted transcriptome analysis of liver and muscle tissues under normal (NT, 5°C) vs. warm (HT, 23°C) conditions to identify heat stress–induced genes and gene categories. We observed a total of 1987 contigs with N50 of 0.46 Mbp, with the largest contig (3.03 Mbp) in the assembled genome. A total of 20,644 protein-coding genes were predicted, and 19,224 genes were functionally annotated: 15,955 genes for Gene Ontology terms and 11,560 genes for KEGG Orthology. We conducted the lost and gained genes analysis compared with three species that: human, zebrafish, and salmon. In the lost genes analysis, we detected that smelt lost 4461 (22.16%), 2825 (10.62%), and 1499 (3.09%) genes compare with above three species, respectively. In the gained genes analysis, we observed that smelt gained 1133 (5.49%), 1670 (8.09%), and 229 (1.11%) genes compared with the above species, respectively. From transcriptome analysis, a total of 297 and 331 differentially expressed genes (DEGs) with a false discovery rate <0.05 were identified in the liver and muscle tissues, respectively. Gene enrichment analysis of DEGs indicates that upregulated genes were significantly enriched for lipid biosynthetic process (GO:0008610, P < 0.001) and regulation of apoptotic process (GO:0042981, P < 0.01), and genes were downregulated by immune responses such as myeloid cell differentiation (GO:0030099, P < 0.001) in the liver under heat stress. In muscle tissue, upregulated genes were enriched for hypoxia (GO:0001666, P < 0.05), transcription regulator activity (GO:0140110, P < 0.001), and calcium-release channel activity (GO:0015278, P < 0.01), and genes were downregulated for a nicotinamide nucleotide biosynthetic process (GO:0019359, P < 0.01). The results of KEGG pathway analysis were similar to that of gene enrichment analysis. The draft genome and transcriptomic of H. nipponensis will be a useful genetic resource for functional and evolutionary studies. Our findings will improve understanding of molecular mechanisms and heat responses and be useful for predicting survival of the smelt and its closely related species under global warming.
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Affiliation(s)
- Biao Xuan
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Kangwon-do, Republic of Korea.,Laboratory of Microbial Genomics and Big Data, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Kangwon-do, Republic of Korea
| | - Jongbin Park
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Kangwon-do, Republic of Korea.,Laboratory of Microbial Genomics and Big Data, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Kangwon-do, Republic of Korea
| | - Sukjung Choi
- Laboratory of Microbial Genomics and Big Data, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Kangwon-do, Republic of Korea
| | - Inhwan You
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Kangwon-do, Republic of Korea.,Laboratory of Microbial Genomics and Big Data, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Kangwon-do, Republic of Korea
| | - Bo-Hye Nam
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Korea
| | - Eun Soo Noh
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Korea
| | - Eun Mi Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Korea
| | - Mi-Young Song
- Inland Fisheries Research Institute, National Institute of Fisheries Science, Gapyeong 12453, Korea
| | - Younhee Shin
- Research and Development Center, Insilicogen Inc, Yongin 16954, Republic of Korea
| | - Ji-Hyeon Jeon
- Research and Development Center, Insilicogen Inc, Yongin 16954, Republic of Korea.,Department of Biological Science, Sungkyunkwan University, Suwon 16419, Korea
| | - Eun Bae Kim
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Kangwon-do, Republic of Korea.,Laboratory of Microbial Genomics and Big Data, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Kangwon-do, Republic of Korea
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Moturi J, Kim KY, Hosseindoust A, Lee JH, Xuan B, Park J, Kim EB, Kim JS, Chae BJ. Author Correction: Effects of Lactobacillus salivarius isolated from feces of fast-growing pigs on intestinal microbiota and morphology of suckling piglets. Sci Rep 2021; 11:9062. [PMID: 33883674 PMCID: PMC8060264 DOI: 10.1038/s41598-021-88639-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Joseph Moturi
- Department of Animal Industry Convergence, Kangwon National University, Chuncheon, 24341, Republic of Korea.,Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Kwang Yeol Kim
- Poultry Research Institute, National Institute of Animal Science, Pyeongchang, 25342, Republic of Korea
| | - Abdolreza Hosseindoust
- Department of Animal Resource Science, College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Jun Hyung Lee
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Biao Xuan
- Department of Applied Animal Science, College of Animal Life Science, Kangwon National University, Chuncheon, Kangwon‑do, Republic of Korea
| | - Jongbin Park
- Department of Applied Animal Science, College of Animal Life Science, Kangwon National University, Chuncheon, Kangwon‑do, Republic of Korea
| | - Eun Bae Kim
- Department of Applied Animal Science, College of Animal Life Science, Kangwon National University, Chuncheon, Kangwon‑do, Republic of Korea
| | - Jin Soo Kim
- Department of Animal Industry Convergence, Kangwon National University, Chuncheon, 24341, Republic of Korea. .,Kangwon National University, Chuncheon, 24341, Republic of Korea.
| | - Byung Jo Chae
- Department of Animal Resource Science, College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
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Moturi J, Kim KY, Hosseindoust A, Lee JH, Xuan B, Park J, Kim EB, Kim JS, Chae BJ. Effects of Lactobacillus salivarius isolated from feces of fast-growing pigs on intestinal microbiota and morphology of suckling piglets. Sci Rep 2021; 11:6757. [PMID: 33762614 PMCID: PMC7990948 DOI: 10.1038/s41598-021-85630-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 02/15/2021] [Indexed: 12/17/2022] Open
Abstract
The study determined the effects of Lactobacillus salivarius (LS) administered early in the life of suckling piglets on their growth performance, gut morphology, and gut microbiota. Thirty litters of 3-day-old crossbreed piglets were randomly assigned to one of the three treatments, and treatments were commenced on day 3 after birth. During the whole period of the experiment, the piglets were kept with their mothers and left to suckle ad libitum while being supplemented with a milk formula with or without the bacterial probiotic supplemented. The control group (CON) was not treated with probiotics, the HLS group was treated with LS144 (HLS) screened from feces of fast-growing pigs with high body mass index (BMI) while the NLS group was supplemented with LS160 (NLS) screened from feces obtained from pigs of normal BMI. At the weaning time, a higher abundance of Actinobacteria, Lentisphaerae, and Elusimicrobia phyla were observed in NLS piglets, whereas the abundance of Fibrobacteres phylum was significantly reduced in NLS and HLS piglets compared with the CON. A greater abundance of Lactobacillus was detected in the HLS treatment compared with the CON. The abundance of Bacteroides and Fibrobacter was higher in the CON piglets compared with the HLS and NLS piglets. Compared with the CON group, the oral administration of LS significantly increased the number of Lactobacillus and villus height in the duodenum, jejunum, and ileum. Moreover, the villus height of the duodenum was significantly improved in the HLS treatment compared with the NLS treatment. Based on the findings in the neonatal piglet model, we suggest that oral supplementation of LS, particularly LS isolated from high BMI pigs, could be beneficial by improving the intestinal villus height.
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Affiliation(s)
- Joseph Moturi
- Department of Animal Industry Convergence, Kangwon National University, Chuncheon, 24341, Republic of Korea.,Department of Bio-Health Convergence, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Kwang Yeol Kim
- Poultry Research Institute, National Institute of Animal Science, Pyeongchang, 25342, Republic of Korea
| | - Abdolreza Hosseindoust
- Department of Animal Resource Science, College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Jun Hyung Lee
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Biao Xuan
- Department of Applied Animal Science, College of Animal Life Science, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea
| | - Jongbin Park
- Department of Applied Animal Science, College of Animal Life Science, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea
| | - Eun Bae Kim
- Department of Applied Animal Science, College of Animal Life Science, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea
| | - Jin Soo Kim
- Department of Animal Industry Convergence, Kangwon National University, Chuncheon, 24341, Republic of Korea. .,Department of Bio-Health Convergence, Kangwon National University, Chuncheon, 24341, Republic of Korea.
| | - Byung Jo Chae
- Department of Animal Resource Science, College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
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Park J, Kim EB. Insights into the Gut and Skin Microbiome of Freshwater Fish, Smelt (Hypomesus nipponensis). Curr Microbiol 2021; 78:1798-1806. [PMID: 33738530 DOI: 10.1007/s00284-021-02440-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 03/01/2021] [Indexed: 12/19/2022]
Abstract
Freshwater smelt (Hypomesus nipponensis) is a planktivorous fish found in the river of South Korea, Japan, China, and Russia. Because of its specific characteristics living in the cold temperature, this species is economically valuable in the various countries that held winter festival. The body size of the smelt is too small, so people consumed raw smelt during the winter festival sometimes. However, the microbial studies of smelt are nonexistent. Here, we characterized and compared the bacterial communities in the gut and skin of freshwater smelts. We amplified, sequenced, and analyzed the V4 regions of bacterial 16S rRNA genes from freshwater smelts. The microbial diversity in the skin (375 OTUs) was much greater than that in the gut (250 OTUs). At the phylum level, Proteobacteria (gut: 51.5%; skin: 52.9%), Firmicutes (gut: 30.6%; skin: 25.4%), Bacteroidetes (gut: 7.7%; skin: 14.7%), and Actinobacteria (gut: 5.2%; skin: 3.8%) were predominant in both organs. At the genus level, Sphingomonas (gut: 24.9%; skin: 4.4%, P < 0.01) was more abundant in the gut, whereas Acinetobacter (gut: 0.8%; skin: 11.8%, P = 0.02) and Pseudomonas (gut: 0.3%; skin: 2.1%, P = 0.01) were more abundant in the skin. Both beneficial (Lactobacillus) and harmful (Staphylococcus and Streptococcus) bacteria were detected in both organs, even under freshwater conditions. These results revealed that smelts have their own unique microbial communities in the gut and skin. Our findings broaden the understanding of planktivorous freshwater fish microbiomes and provide new insights into fish microbiomes for ensuring food safety.
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Affiliation(s)
- Jongbin Park
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, 24341, Kangwon-do, Republic of Korea
| | - Eun Bae Kim
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, 24341, Kangwon-do, Republic of Korea. .,Department of Animal Life Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea.
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Jeong Y, Park J, Kim EB. Changes in Gut Microbial Community of Pig Feces in Response to Different Dietary Animal Protein Media. J Microbiol Biotechnol 2020; 30:1321-1334. [PMID: 32522966 PMCID: PMC9728240 DOI: 10.4014/jmb.2003.03021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/07/2020] [Accepted: 05/28/2020] [Indexed: 12/15/2022]
Abstract
Beef, pork, chicken and milk are considered representative protein sources in the human diet. Since the digestion of protein is important, the role of intestinal microflora is also important. Despite this, the pure effects of meat and milk intake on the microbiome are yet to be fully elucidated. To evaluate the effect of beef, pork, chicken and milk on intestinal microflora, we observed changes in the microbiome in response to different types of dietary animal proteins in vitro. Feces were collected from five 6-week-old pigs. The suspensions were pooled and inoculated into four different media containing beef, pork, chicken, or skim milk powder in distilled water. Changes in microbial communities were analyzed using 16S rRNA sequencing. The feces alone had the highest microbial alpha diversity. Among the treatment groups, beef showed the highest microbial diversity, followed by pork, chicken, and milk. The three dominant phyla were Proteobacteria, Firmicutes, and Bacteroidetes in all the groups. The most abundant genera in beef, pork, and chicken were Rummeliibacillus, Clostridium, and Phascolarctobacterium, whereas milk was enriched with Streptococcus, Lactobacillus, and Enterococcus. Aerobic bacteria decreased while anaerobic and facultative anaerobic bacteria increased in protein-rich nutrients. Functional gene groups were found to be over-represented in protein-rich nutrients. Our results provide baseline information for understanding the roles of dietary animal proteins in reshaping the gut microbiome. Furthermore, growth-promotion by specific species/genus may be used as a cultivation tool for uncultured gut microorganisms.
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Affiliation(s)
- Yujeong Jeong
- Department of Applied Animal Science, College of Animal Life Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Jongbin Park
- Department of Animal Life Science, College of Animal Life Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Eun Bae Kim
- Department of Applied Animal Science, College of Animal Life Science, Kangwon National University, Chuncheon 24341, Republic of Korea,Department of Animal Life Science, College of Animal Life Science, Kangwon National University, Chuncheon 24341, Republic of Korea,Corresponding author Phone: +82-33-250-8642 Fax: +82-33-259-5574 E-mail:
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Park J, Kim SJ, Kim EB. Changes in the Microbial Community of the Mottled Skate ( Beringraja pulchra) During Alkaline Fermentation. J Microbiol Biotechnol 2020; 30:1195-1206. [PMID: 32423184 PMCID: PMC9728196 DOI: 10.4014/jmb.2003.03024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/06/2020] [Indexed: 12/15/2022]
Abstract
Beringraja pulchra, Cham-hong-eo in Korean, is a mottled skate which is belonging to the cartilaginous fish. Although this species is economically valuable in South Korea as an alkalinefermented food, there are few microbial studies on such fermentation. Here, we analyzed microbial changes and pH before, during, and after fermentation and examined the effect of inoculation by a skin microbiota mixture on the skate fermentation (control vs. treatment). To analyze microbial community, the V4 regions of bacterial 16S rRNA genes from the skates were amplified, sequenced and analyzed. During the skate fermentation, pH and total number of marine bacteria increased in both groups, while microbial diversity decreased after fermentation. Pseudomonas, which was predominant in the initial skate, declined by fermentation (Day 0: 11.39 ± 5.52%; Day 20: 0.61 ± 0.9%), while the abundance of Pseudoalteromonas increased dramatically (Day 0: 1.42 ± 0.41%; Day 20: 64.92 ± 24.15%). From our co-occurrence analysis, the Pseudoalteromonas was positively correlated with Aerococcaceae (r = 0.638) and Moraxella (r = 0.474), which also increased with fermentation, and negatively correlated with Pseudomonas (r = -0.847) during fermentation. There are no critically significant differences between control and treatment. These results revealed that the alkaline fermentation of skates dramatically changed the microbiota, but the initial inoculation by a skin microbiota mixture didn't show critical changes in the final microbial community. Our results extended understanding of microbial interactions and provided the new insights of microbial changes during alkaline fermentation.
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Affiliation(s)
- Jongbin Park
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Soo Jin Kim
- Department of Animal Life Science, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Eun Bae Kim
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea,Department of Animal Life Science, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea,Corresponding author Phone: +82-33-250-8642 Fax: +82-33-259-5574 E-mail:
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12
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You I, Kim EB. Genome-based species-specific primers for rapid identification of six species of Lactobacillus acidophilus group using multiplex PCR. PLoS One 2020; 15:e0230550. [PMID: 32196527 PMCID: PMC7083307 DOI: 10.1371/journal.pone.0230550] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 03/04/2020] [Indexed: 12/21/2022] Open
Abstract
Many Lactobacillus species are frequently isolated from dairy products, animal guts, and the vaginas of healthy women. However, sequencing-based identification of isolated Lactobacillus strain is time/cost-consuming and lobor-intensive. In this study, we developed a multiplex PCR method to distinguish six closely related species in the Lactobacillus acidophilus group (L. gasseri, L. acidophilus, L. helveticus, L. jensenii, L. crispatus, and L. gallinarum), which is based on species-specific primer sets. Altogether, 86 genomes of 9 Lactobacillus species from the National Center of Biotechnology Information (NCBI) database were compared to detect species-specific genes and design six species-specific primer sets. The PCR conditions of the individual primer sets were optimized via gradient PCR methods. A final multiplex PCR condition was also optimized for a mixture of all six primer sets mixed. When identifying a single strain, the optimized multiplex PCR method can specifically detect one of the six species, but no band was amplified at least from the other Lactobacillus and Enterococcus species. These results indicated that species-specific primer sets designed from the genome comparison could identify one strain within the six Lactobacillus species by a single PCR reaction. Using the method described here, we will be able to save time, cost, and labor during species identification and screening of commercially important probiotic lactobacilli.
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Affiliation(s)
- Inhwan You
- Department of Animal Life Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, Republic of Korea
| | - Eun Bae Kim
- Department of Animal Life Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, Republic of Korea
- Institute of Animal Resources, Kangwon National University, Chuncheon, Republic of Korea
- * E-mail:
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13
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Park J, Kim EB. Differences in microbiome and virome between cattle and horses in the same farm. Asian-Australas J Anim Sci 2019; 33:1042-1055. [PMID: 32054207 PMCID: PMC7206377 DOI: 10.5713/ajas.19.0267] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/28/2019] [Indexed: 02/06/2023]
Abstract
Objective The ecosystem of an animal farm is composed of various elements, such as animals, farmers, plants, feed, soil, and microorganisms. A domesticated animal’s health is largely connected with the reservoir of bacteria and viruses in animal farms. Although a few studies have focused on exploring the gut microbiome of animals, communities of microbiota and viruses in feedlots have not been thoroughly investigated. Methods Here, we collected feces and dust samples (4 groups: cattle feces, C_F; horse feces, H_F; cattle dust, C_D; and horse dust, H_D) from cattle and horse farms sharing the same housing and investigated their microbiome/virome communities by Illumina sequencing. Results Dust groups (C_D and H_D) showed higher microbial diversity than feces groups (C_F and H_F) regardless of animal species. From the microbial community analysis, all the samples from the four groups have major phyla such as Proteobacteria (min 37.1% to max 42.8%), Firmicutes (19.1% to 24.9%), Bacteroidetes (10.6% to 22.1%), and Actinobacteria (6.1% to 20.5%). The abundance of Streptococcus, which commonly recognized as equine pathogens, was significantly higher in the horse group (H_D and H_F). Over 99% among the classified virome reads were classified as Caudovirales, a group of tailed bacteriophages, in all four groups. Foot-and-mouth disease virus and equine adenovirus, which cause deadly diseases in cattle and horse, respectively, were not detected. Conclusion Our results will provide baseline information to understand different gut and environmental microbial ecology between two livestock species.
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Affiliation(s)
- Jongbin Park
- Department of Animal Life Science, College of Animal Life Science, Kangwon National University, Chuncheon 24341, Korea
| | - Eun Bae Kim
- Department of Animal Life Science, College of Animal Life Science, Kangwon National University, Chuncheon 24341, Korea.,Department of Applied Animal Science, College of Animal Life Science, Kangwon National University, Chuncheon 24341, Korea
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14
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Choi S, Kim EB. Complete mitochondrial genome sequence and SNPs of the Korean smelt Hypomesus nipponensis (Osmeriformes, Osmeridae). Mitochondrial DNA Part B 2019. [DOI: 10.1080/23802359.2019.1613178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Sukjung Choi
- Laboratory of Microbial Genomics and Big Data, College of Animal Life Sciences, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea
| | - Eun Bae Kim
- Laboratory of Microbial Genomics and Big Data, College of Animal Life Sciences, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea
- Division of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea
- Department of Animal Life Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea
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15
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Affiliation(s)
- Sukjung Choi
- Laboratory of Microbial Genomics and Big Data, College of Animal Life Sciences, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea
| | - Soo Jin Kim
- Laboratory of Microbial Genomics and Big Data, College of Animal Life Sciences, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea
- Division of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea
| | - Eun Bae Kim
- Laboratory of Microbial Genomics and Big Data, College of Animal Life Sciences, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea
- Division of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea
- Department of Animal Life Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea
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16
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Utama DT, Park J, Kim DS, Kim EB, Lee SK. Effect of Ground Chopi ( Zanthoxylum piperitum) on Physicochemical Traits and Microbial Community of Chicken Summer Sausage during Manufacture. Korean J Food Sci Anim Resour 2018; 38:936-949. [PMID: 30479501 PMCID: PMC6238041 DOI: 10.5851/kosfa.2018.e26] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/17/2018] [Accepted: 07/31/2018] [Indexed: 02/01/2023] Open
Abstract
Changes in microbial community and physicochemical traits of chicken summer sausage made from spent layer thigh added with different level (0%, 0.1%, 0.3%, and 0.5% w/w) of ground chopi (Zanthoxylum piperitum) during manufacture were analyzed. The microbial community was profiled and analyzed by sequencing 16S rRNA gene using Illumina MiSeq. Samples were taken from raw sausage batter, after 15 h of fermentation, 8 h of cooking including cooling down, and 7 d of drying. The final pH of the sausage was reduced by the addition of ground chopi. However, no clear effect on water activity was observed. Ground chopi inhibited the development of red curing color after fermentation as it exhibited antimicrobial effect. However, the effect on species richness and microbial composition after cooking was unclear. Ground chopi delayed lipid oxidation during manufacture and the effect was dependent on the addition level. Fermentation reduced the species richness with a dominancy of lactic acid bacteria. The profile of microbiota in the raw batter was different from other stages, while the closest relationship was observed after cooking and drying. Proteobacteria was predominant, followed by Firmicutes and Bacteroidetes in raw samples. Firmicutes became dominating after fermentation and so forth, whereas other predominant phylum decreased. At genus level, unclassified Lactobacillales was the most abundant group found after fermentation and so forth. Therefore, the overall microbial composition aspects were mainly controlled during fermentation by the abundance of lactic acid bacteria, while bacterial counts and lipid oxidation were controlled by cooking and the addition of ground chopi.
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Affiliation(s)
- Dicky Tri Utama
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Korea
| | - Jongbin Park
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Korea
| | - Dong Soo Kim
- Quality Assurance Team, Pulmuone Co., Ltd., Daeso 27671, Korea
| | - Eun Bae Kim
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Korea
| | - Sung Ki Lee
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Korea
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17
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Choi S, Jin GD, Park J, You I, Kim EB. Pan-Genomics of Lactobacillus plantarum Revealed Group-Specific Genomic Profiles without Habitat Association. J Microbiol Biotechnol 2018; 28:1352-1359. [DOI: 10.4014/jmb.1803.03029] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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18
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Bharanidharan R, Arokiyaraj S, Kim EB, Lee CH, Woo YW, Na Y, Kim D, Kim KH. Ruminal methane emissions, metabolic, and microbial profile of Holstein steers fed forage and concentrate, separately or as a total mixed ration. PLoS One 2018; 13:e0202446. [PMID: 30110381 PMCID: PMC6093700 DOI: 10.1371/journal.pone.0202446] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 08/02/2018] [Indexed: 12/15/2022] Open
Abstract
Few studies have examined the effects of feeding total mixed ration (TMR) versus roughage and concentrate separately (SF) on ruminant methane production. Therefore, this study compared differences in methane production, ruminal characteristics, total tract digestibility of nutrients, and rumen microbiome between the two feeding methods in Holstein steers. A total six Holstein steers of initial bodyweights 540 ± 34 kg were divided into two groups and assigned to a same experimental diet with two different feeding systems (TMR or SF) in a crossover design with 21 d periods. The experimental diet contained 73% concentrate and 27% forage and were fed twice a day. The total tract digestibility of crude protein, neutral detergent fibre, and organic matter were not affected by the two different feeding systems. Steers fed TMR emitted more methane (138.5 vs. 118.2 L/d; P < 0.05) and lost more gross energy as methane energy (4.0 vs. 3.5% gross energy intake; P = 0.005) compared to those fed SF. Steers fed TMR had greater (P < 0.05) total volatile fatty acid (VFA), ammonia-N concentrations and propionate proportion of total VFA at 1.5 h, whereas lower after that compared to steers fed SF. The greater (P < 0.05) acetate: propionate ratio at 4.5 h for steers fed TMR reflected the shift of H2 sink from propionate towards acetate synthesis. The lower (P < 0.05) isobutyrate and isovalerate proportions of total VFA observed in steers fed TMR implies decrease in net consumption of H2 for microbial protein synthesis compared to SF. There were no differences in both major bacterial and archaeal diversity between TMR and SF, unlike several minor bacterial abundances. The minor groups such as Coprococcus, Succiniclasticum, Butyrivibrio, and Succinivibrio were associated with the changes in ruminal VFA profiles or methanogenesis indirectly. Overall, these results indicate that SF reduces methane emissions from ruminants and increases propionate proportion of total VFA without affecting total tract digestion compared to TMR. There were no evidences that the response differed due to different major underlying microbial population.
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Affiliation(s)
- Rajaraman Bharanidharan
- Department of International Agricultural Technology, Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang, Gangwon, The Republic of Korea
| | - Selvaraj Arokiyaraj
- Department of Ecofriendly Livestock Science, Institute of Green Bio Science and Technology, Seoul National University, Pyeongchang, Gangwon, The Republic of Korea
| | - Eun Bae Kim
- Department of Animal Life Science, Kangwon National University, Chuncheon, The Republic of Korea
| | - Chang Hyun Lee
- Department of Animal Science and Technology, Konkuk University, Seoul, The Republic of Korea
| | - Yang Won Woo
- Department of Ecofriendly Livestock Science, Institute of Green Bio Science and Technology, Seoul National University, Pyeongchang, Gangwon, The Republic of Korea
| | - Youngjun Na
- Department of Animal Science and Technology, Konkuk University, Seoul, The Republic of Korea
| | - Danil Kim
- Department of Ecofriendly Livestock Science, Institute of Green Bio Science and Technology, Seoul National University, Pyeongchang, Gangwon, The Republic of Korea
- Department of Farm Animal Medicine, College of Veterinary Medicine, Seoul National University, Seoul, The Republic of Korea
| | - Kyoung Hoon Kim
- Department of International Agricultural Technology, Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang, Gangwon, The Republic of Korea
- Department of Ecofriendly Livestock Science, Institute of Green Bio Science and Technology, Seoul National University, Pyeongchang, Gangwon, The Republic of Korea
- * E-mail:
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19
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Yeo S, Shin HS, Lee HW, Hong D, Park H, Holzapfel W, Kim EB, Huh CS. Determination of Optimized Growth Medium and Cryoprotective Additives to Enhance the Growth and Survival of Lactobacillus salivarius. J Microbiol Biotechnol 2018; 28:718-731. [DOI: 10.4014/jmb.1801.01059] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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20
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Han GG, Lee JY, Jin GD, Park J, Choi YH, Kang SK, Chae BJ, Kim EB, Choi YJ. Tracing of the fecal microbiota of commercial pigs at five growth stages from birth to shipment. Sci Rep 2018; 8:6012. [PMID: 29662088 PMCID: PMC5902624 DOI: 10.1038/s41598-018-24508-7] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 04/03/2018] [Indexed: 12/30/2022] Open
Abstract
The intestinal microbiota affect various physiological traits of host animals such as brain development, obesity, age, and the immune system. In the swine industry, understanding the relationship between intestinal microbiota and growth stage is essential because growth stage is directly related to the feeding system of pigs, thus we studied the intestinal microbiota of 32 healthy pigs across five sows at 10, 21, 63, 93, and 147 d of ages. The intestinal microbiota were altered with growth of pigs and were separated into three distinct clusters. The relative abundance of several phyla and genera were significantly different between growth stages. We observed co-occurrence pattern of the intestinal microbiota at each growth stage. In addition, we predicted the functions of the intestinal microbiota and confirmed that several KEGG pathways were significantly different between growth stages. We also explored the relationship between the intestinal microbiota and innate factors such as the maternal effect and gender. When pigs were young, innate factors affected on construction of intestinal microbiota, however this tendency was disappeared with growth. Our findings broaden the understanding of microbial ecology, and the results will be used as a reference for investigating host-microbe interactions in the swine industry.
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Affiliation(s)
- Geon Goo Han
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, Republic of Korea
| | - Jun-Yeong Lee
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, Republic of Korea
| | - Gwi-Deuk Jin
- Department of Animal Life Science, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Jongbin Park
- Department of Animal Life Science, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Yo Han Choi
- Department of Animal Life Science, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Sang-Kee Kang
- Institute of Green-Bio Science & Technology, Seoul National University, Pyeongchang, Gangwon-do, Republic of Korea
| | - Byung Jo Chae
- Department of Animal Life Science, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Eun Bae Kim
- Department of Animal Life Science, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea. .,Division of Applied Animal Science, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea.
| | - Yun-Jaie Choi
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, Republic of Korea.
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21
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Ahn H, Lee C, Nam BH, Kim EB, Caetano-Anolles K, Kim H. Selective pressure on the protein-coding genes of the pufferfish is correlated with phenotypic traits. Mar Genomics 2017; 37:182-186. [PMID: 29273445 DOI: 10.1016/j.margen.2017.11.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 11/04/2017] [Accepted: 11/29/2017] [Indexed: 11/28/2022]
Abstract
The pufferfish accumulates neurotoxic tetrodotoxin in its body and inflates by filling its stomach with water. These traits are unique to this species, and may be a result of adaptation post-divergence of Tetraodontidae. However, evolution of the protein-coding genes in the pufferfish has not yet been well elucidated. Detection of positive selection on these genes can help us understand the mechanisms associated with functional evolution. We downloaded well-annotated gene information of two pufferfish species, Takifugu rubripes and Tetraodon nigroviridis, from the public ENSEMBL database. In order to detect selective pressure on protein-coding sequences, we performed dN/dS estimation using codeml within the PAML software package. We selected one to one orthologous genes among seven fish species (Gasterosteus aculeatus, Oryzias latipes, Poecilia formosa, Takifugu rubripes, Tetraodon nigroviridis, and Xiphophorus maculatus). Results of dN/dS analysis on orthologous genes indicate that pufferfish showed high non-synonymous substitution rate for positively selected genes, and the evolutionary rate was faster during the diversification of two pufferfishes after divergence. Additionally, a candidate mechanism for regulation of neuro-toxicity of tetrodotoxin was identified from functional annotation of positively selected genes. These results support positive selection on protein-coding genes of the pufferfish with the acquisition of specific phenotypic traits.
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Affiliation(s)
- Hyeonju Ahn
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-742, Republic of Korea
| | - Chul Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Republic of Korea
| | - Bo-Hye Nam
- Biotechnology Research Division, National Fisheries Research & Development Institute, Busan 619-705, Republic of Korea
| | - Eun Bae Kim
- Department of Animal Life Science, Kangwon National University, Chuncheon 200-701, Republic of Korea
| | - Kelsey Caetano-Anolles
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-742, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-742, Republic of Korea.
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22
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Lee JY, Han GG, Kim EB, Choi YJ. Comparative genomics of Lactobacillus salivarius strains focusing on their host adaptation. Microbiol Res 2017; 205:48-58. [DOI: 10.1016/j.micres.2017.08.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 07/25/2017] [Accepted: 08/12/2017] [Indexed: 01/15/2023]
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23
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Lee JY, Han GG, Lee HB, Lee SM, Kang SK, Jin GD, Park J, Chae BJ, Choi YH, Kim EB, Choi YJ. Prohibition of antibiotic growth promoters has affected the genomic profiles of Lactobacillus salivarius inhabiting the swine intestine. PLoS One 2017; 12:e0186671. [PMID: 29059217 PMCID: PMC5653324 DOI: 10.1371/journal.pone.0186671] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 10/05/2017] [Indexed: 12/30/2022] Open
Abstract
After the introduction of a ban on the use of antibiotic growth promoters (AGPs) for livestock, the feeding environment, including the composition of animal intestinal microbiota, has changed rapidly. We hypothesized that the microbial genomes have also been affected by this legal prohibition, and investigated an important member of the swine gut microbiota, Lactobacillus salivarius, with a pan-genomic approach. Here, we isolated 21 L. salivarius strains composed of 6 strains isolated before the AGP prohibition (SBPs) and 15 strains isolated after the AGP prohibition (SAPs) at an interval of a decade, and the draft genomes were generated de novo. Several genomic differences between SBPs and SAPs were identified, although the number and function of antibiotic resistance genes were not different. SBPs showed larger genome size and a higher number of orthologs, as well as lower genetic diversity, than SAPs. SBPs had genes associated with the utilization of L-rhamnose and D-tagatose for energy production. Because these sugars are also used in exopolysaccharide (EPS) synthesis, we tried to identify differences in biofilm formation-associated genes. The genes for the production of EPSs and extracellular proteins were different in terms of amino acid sequences. Indeed, SAPs formed dense biofilm and survived better than SBPs in the swine intestinal environment. These results suggest that SAPs have evolved and adapted to protect themselves from new selection pressure of the swine intestinal microenvironment by forming dense biofilms, adopting a distinct antibiotic resistance strategy. This finding is particularly important to understand the evolutionary changes in host-microbe interaction and provide detailed insight for the development of effective probiotics for livestock.
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Affiliation(s)
- Jun-Yeong Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Geon Goo Han
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Ho-Bin Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Sang-Mok Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Sang-Kee Kang
- Institute of Green-Bio Science & Technology, Seoul National University, Pyeongchang, Republic of Korea
| | - Gwi-Deuk Jin
- Department of Animal Life Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Jongbin Park
- Department of Animal Life Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Byung Jo Chae
- Department of Animal Life Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Yo Han Choi
- Department of Animal Life Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Eun Bae Kim
- Department of Animal Life Science, Kangwon National University, Chuncheon, Republic of Korea
- * E-mail: (YJC); (EBK)
| | - Yun-Jaie Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
- Research Institute for Agriculture and Life Science, Seoul National University, Seoul, Republic of Korea
- * E-mail: (YJC); (EBK)
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Lee JY, Han GG, Choi J, Jin GD, Kang SK, Chae BJ, Kim EB, Choi YJ. Pan-Genomic Approaches in Lactobacillus reuteri as a Porcine Probiotic: Investigation of Host Adaptation and Antipathogenic Activity. Microb Ecol 2017; 74:709-721. [PMID: 28439658 DOI: 10.1007/s00248-017-0977-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 03/24/2017] [Indexed: 06/07/2023]
Abstract
After the introduction of a ban on the use of antibiotic growth promoters (AGPs) for livestock, reuterin-producing Lactobacillus reuteri is getting attention as an alternative to AGPs. In this study, we investigated genetic features of L. reuteri associated with host specificity and antipathogenic effect. We isolated 104 L. reuteri strains from porcine feces, and 16 strains, composed of eight strains exhibiting the higher antipathogenic effect (group HS) and eight strains exhibiting the lower effect (group LS), were selected for genomic comparison. We generated draft genomes of the 16 isolates and investigated their pan-genome together with the 26 National Center for Biotechnology Information-registered genomes. L. reuteri genomes organized six clades with multi-locus sequence analysis, and the clade IV includes the 16 isolates. First, we identified six L. reuteri clade IV-specific genes including three hypothetical protein-coding genes. The three annotated genes encode transposases and cell surface proteins, indicating that these genes are the result of adaptation to the host gastrointestinal epithelia and that these host-specific traits were acquired by horizontal gene transfer. We also identified differences between groups HS and LS in the pdu-cbi-cob-hem gene cluster, which is essential for reuterin and cobalamin synthesis, and six genes specific to group HS are revealed. While the strains of group HS possessed all genes of this cluster, LS strains have lost many genes of the cluster. This study provides a deeper understanding of the relationship between probiotic properties and genomic features of L. reuteri.
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Affiliation(s)
- Jun-Yeong Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Geon Goo Han
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Jaeyun Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Gwi-Deuk Jin
- Department of Animal Life Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Sang-Kee Kang
- Institute of Green-Bio Science and Technology, Seoul National University, Pyeongchang, Republic of Korea
| | - Byung Jo Chae
- Department of Animal Life Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Eun Bae Kim
- Department of Animal Life Science, Kangwon National University, Chuncheon, Republic of Korea.
| | - Yun-Jaie Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea.
- Research Institute for Agriculture and Life Science, Seoul National University, Seoul, Republic of Korea.
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Lee SG, Kaya A, Avanesov AS, Podolskiy DI, Song EJ, Go DM, Jin GD, Hwang JY, Kim EB, Kim DY, Gladyshev VN. Age-associated molecular changes are deleterious and may modulate life span through diet. Sci Adv 2017; 3:e1601833. [PMID: 28232953 PMCID: PMC5315447 DOI: 10.1126/sciadv.1601833] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 11/29/2016] [Indexed: 05/15/2023]
Abstract
Transition through life span is accompanied by numerous molecular changes, such as dysregulated gene expression, altered metabolite levels, and accumulated molecular damage. These changes are thought to be causal factors in aging; however, because they are numerous and are also influenced by genotype, environment, and other factors in addition to age, it is difficult to characterize the cumulative effect of these molecular changes on longevity. We reasoned that age-associated changes, such as molecular damage and tissue composition, may influence life span when used in the diet of organisms that are closely related to those that serve as a dietary source. To test this possibility, we used species-specific culture media and diets that incorporated molecular extracts of young and old organisms and compared the influence of these diets on the life span of yeast, fruitflies, and mice. In each case, the "old" diet or medium shortened the life span for one or both sexes. These findings suggest that age-associated molecular changes, such as cumulative damage and altered dietary composition, are deleterious and causally linked with aging and may affect life span through diet.
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Affiliation(s)
- Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Bioinspired Science, Ewha Womans University, Seoul 03760, South Korea
| | - Alaattin Kaya
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Andrei S. Avanesov
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Dmitriy I. Podolskiy
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Eun Ju Song
- Ewha Laboratory Animal Genomic Center, Institute of Molecular Life Sciences and Technology, Office of Research Affairs, Ewha Womans University, Seoul 03760, South Korea
- Department of Veterinary Physiology, College of Veterinary Medicine, BK21 PLUS Creative Veterinary Research Center, Seoul National University, Seoul 08826, South Korea
| | - Du-Min Go
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Seoul National University, Seoul 08826, South Korea
| | - Gwi-Deuk Jin
- Department of Animal Life Science, Kangwon National University, Chuncheon 24341, South Korea
| | - Jae Yeon Hwang
- Department of Animal Life Science, Kangwon National University, Chuncheon 24341, South Korea
| | - Eun Bae Kim
- Department of Animal Life Science, Kangwon National University, Chuncheon 24341, South Korea
- Division of Applied Animal Science, Kangwon National University, Chuncheon 24341, South Korea
| | - Dae-Yong Kim
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Seoul National University, Seoul 08826, South Korea
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Corresponding author.
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Kieffer DA, Piccolo BD, Marco ML, Kim EB, Goodson ML, Keenan MJ, Dunn TN, Knudsen KEB, Martin RJ, Adams SH. Mice Fed a High-Fat Diet Supplemented with Resistant Starch Display Marked Shifts in the Liver Metabolome Concurrent with Altered Gut Bacteria. J Nutr 2016; 146:2476-2490. [PMID: 27807042 PMCID: PMC5118768 DOI: 10.3945/jn.116.238931] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 09/09/2016] [Accepted: 09/27/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND High-amylose-maize resistant starch type 2 (HAMRS2) is a fermentable dietary fiber known to alter the gut milieu, including the gut microbiota, which may explain the reported effects of resistant starch to ameliorate obesity-associated metabolic dysfunction. OBJECTIVE Our working hypothesis was that HAMRS2-induced microbiome changes alter gut-derived signals (i.e., xenometabolites) reaching the liver via the portal circulation, in turn altering liver metabolism by regulating gene expression and other pathways. METHODS We used a multi-omics systems biology approach to characterize HAMRS2-driven shifts to the cecal microbiome, liver metabolome, and transcriptome, identifying correlates between microbial changes and liver metabolites under obesogenic conditions that, to our knowledge, have not previously been recognized. Five-week-old male C57BL/6J mice were fed an energy-dense 45% lard-based-fat diet for 10 wk supplemented with either 20% HAMRS2 by weight (n = 14) or rapidly digestible starch (control diet; n = 15). RESULTS Despite no differences in food intake, body weight, glucose tolerance, fasting plasma insulin, or liver triglycerides, the HAMRS2 mice showed a 15-58% reduction in all measured liver amino acids, except for Gln, compared with control mice. These metabolites were equivalent in the plasma of HAMRS2 mice compared with controls, and transcripts encoding key amino acid transporters were not different in the small intestine or liver, suggesting that HAMRS2 effects were not simply due to lower hepatocyte exposure to systemic amino acids. Instead, alterations in gut microbial metabolism could have affected host nitrogen and amino acid homeostasis: HAMRS2 mice showed a 62% increase (P < 0.0001) in 48-h fecal output and a 41% increase (P < 0.0001) in fecal nitrogen compared with control mice. Beyond amino acid metabolism, liver transcriptomics revealed pathways related to lipid and xenobiotic metabolism; and pathways related to cell proliferation, differentiation, and growth were affected by HAMRS2 feeding. CONCLUSION Together, these differences indicate that HAMRS2 dramatically alters hepatic metabolism and gene expression concurrent with shifts in specific gut bacteria in C57BL/6J mice.
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Affiliation(s)
- Dorothy A Kieffer
- Graduate Group in Nutritional Biology and
- Department of Nutrition
- Obesity and Metabolism Research Unit, USDA-Agricultural Research Service Western Human Nutrition Research Center, Davis, CA
| | - Brian D Piccolo
- Arkansas Children's Nutrition Center and
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR
| | | | - Eun Bae Kim
- Food Science and Technology Department, and
- Department of Animal Life Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | | | | | - Tamara N Dunn
- Graduate Group in Nutritional Biology and
- Department of Nutrition
- Obesity and Metabolism Research Unit, USDA-Agricultural Research Service Western Human Nutrition Research Center, Davis, CA
| | | | - Roy J Martin
- Graduate Group in Nutritional Biology and
- Department of Nutrition
- Obesity and Metabolism Research Unit, USDA-Agricultural Research Service Western Human Nutrition Research Center, Davis, CA
| | - Sean H Adams
- Graduate Group in Nutritional Biology and
- Department of Nutrition
- Arkansas Children's Nutrition Center and
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR
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27
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Kieffer DA, Piccolo BD, Marco ML, Kim EB, Goodson ML, Keenan MJ, Dunn TN, Knudsen KEB, Adams SH, Martin RJ. Obese Mice Fed a Diet Supplemented with Enzyme-Treated Wheat Bran Display Marked Shifts in the Liver Metabolome Concurrent with Altered Gut Bacteria. J Nutr 2016; 146:2445-2460. [PMID: 27798344 DOI: 10.3945/jn.116.238923] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 08/11/2016] [Accepted: 09/09/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Enzyme-treated wheat bran (ETWB) contains a fermentable dietary fiber previously shown to decrease liver triglycerides (TGs) and modify the gut microbiome in mice. It is not clear which mechanisms explain how ETWB feeding affects hepatic metabolism, but factors (i.e., xenometabolites) associated with specific microbes may be involved. OBJECTIVE The objective of this study was to characterize ETWB-driven shifts in the cecal microbiome and to identify correlates between microbial changes and diet-related differences in liver metabolism in diet-induced obese mice that typically display steatosis. METHODS Five-week-old male C57BL/6J mice fed a 45%-lard-based fat diet supplemented with ETWB (20% wt:wt) or rapidly digestible starch (control) (n = 15/group) for 10 wk were characterized by using a multi-omics approach. Multivariate statistical analysis was used to identify variables that were strong discriminators between the ETWB and control groups. RESULTS Body weight and liver TGs were decreased by ETWB feeding (by 10% and 25%, respectively; P < 0.001), and an index of liver reactive oxygen species was increased (by 29%; P < 0.01). The cecal microbiome showed an increase in Bacteroidetes (by 42%; P < 0.05) and a decrease in Firmicutes (by 16%; P < 0.05). Metabolites that were strong discriminators between the ETWB and control groups included decreased liver antioxidants (glutathione and α-tocopherol); decreased liver carbohydrate metabolites, including glucose; lower hepatic arachidonic acid; and increased liver and plasma β-hydroxybutyrate. Liver transcriptomics revealed key metabolic pathways affected by ETWB, especially those related to lipid metabolism and some fed- or fasting-regulated genes. CONCLUSIONS Together, these changes indicate that dietary fibers such as ETWB regulate hepatic metabolism concurrently with specific gut bacteria community shifts in C57BL/6J mice. It is proposed that these changes may elicit gut-derived signals that reach the liver via enterohepatic circulation, ultimately affecting host liver metabolism in a manner that mimics, in part, the fasting state.
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Affiliation(s)
- Dorothy A Kieffer
- Graduate Group in Nutritional Biology and.,Department of Nutrition.,Obesity and Metabolism Research Unit, USDA-Agricultural Research Service Western Human Nutrition Research Center, Davis, CA
| | - Brian D Piccolo
- Arkansas Children's Nutrition Center and.,Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR
| | | | - Eun Bae Kim
- Food Science and Technology Department, and.,Department of Animal Life Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | | | | | - Tamara N Dunn
- Graduate Group in Nutritional Biology and.,Department of Nutrition.,Obesity and Metabolism Research Unit, USDA-Agricultural Research Service Western Human Nutrition Research Center, Davis, CA
| | | | - Sean H Adams
- Graduate Group in Nutritional Biology and .,Department of Nutrition.,Arkansas Children's Nutrition Center and.,Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Roy J Martin
- Graduate Group in Nutritional Biology and .,Department of Nutrition.,Obesity and Metabolism Research Unit, USDA-Agricultural Research Service Western Human Nutrition Research Center, Davis, CA
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Han GG, Lee JY, Jin GD, Park J, Choi YH, Chae BJ, Kim EB, Choi YJ. WITHDRAWN: Evaluating the association between body weight and the intestinal microbiota of weaned piglets via 16S rRNA sequencing. Vet Microbiol 2016; 196:55-62. [PMID: 27939156 DOI: 10.1016/j.vetmic.2016.10.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 10/14/2016] [Indexed: 12/27/2022]
Abstract
This article has been removed: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy).
The publisher regrets that an error occurred due to a technical issue which led to the premature publication of this paper. This error bears no reflection on the article or its authors. The publisher apologizes to the authors and the readers for this unfortunate error.
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Affiliation(s)
- Geon Goo Han
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Jun-Yeong Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Gwi-Deuk Jin
- Department of Animal Life Science, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Jongbin Park
- Department of Animal Life System, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Yo Han Choi
- Department of Animal Life Science, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Byung Jo Chae
- Department of Animal Life Science, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Eun Bae Kim
- Department of Animal Life Science, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea; Division of Applied Animal Science, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea.
| | - Yun-Jaie Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea; Research Institute for Agriculture and Life Science, Seoul National University, Seoul, Republic of Korea.
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29
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So KM, Lee Y, Bok JD, Kim EB, Chung MI. Analysis of Ionomic Profiles of Canine Hairs Exposed to Lipopolysaccharide (LPS)-Induced Stress. Biol Trace Elem Res 2016; 172:364-371. [PMID: 26758868 DOI: 10.1007/s12011-015-0611-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/28/2015] [Indexed: 10/22/2022]
Abstract
The purpose of this study was to provide a new insight on the response of canines to stress exposure; the ionomic profiles of canine hair (2.8 ± 0.3 years, 15.17 ± 2.1 kg) (n = 10) was determined before and after lipopolysaccharide (LPS) injections. LPS was intramuscularly injected to induce inflammatory stress responses which were confirmed by observing increases in the level of serum cortisol, aldosterone, and inflammatory cytokines such as IL-6, IL-1β, and TNF-α. The hair contents of 17 elements were obtained by applying analytical procedures using the inductively coupled plasma mass spectrometry (ICP-MS). The following elements: sodium(Na) and potassium(K) among macro-elements, iron(Fe) and manganese(Mn) among micro-elements, and aluminum(Al), nickel(Ni), and lead(Pb) for toxic elements, showed significant increased levels with the immunological stress. The degree of increase in toxic elements was remarkable with the stress exposure. A forty-five-fold increase seen in Al accumulation with the stress exposure was noteworthy. Although mercury(Hg) and cadmium(Cd) showed decreased levels with the stress exposure, the degree was negligible compared to the level of increase. Correlation pattern between the elements was changed with the immunological stress. Toxic elements became more correlated with macro- or micro-elements than with toxic elements themselves after the stress exposure. Principal component analysis (PCA) showed that LPS challenge shifted the overall hair mineral profiles to a consistent direction changing Al and K up, even in animals with different hair mineral profiles before LPS treatment. In conclusion, the multivariate data processing and study of element distribution patterns provided new information about the ionomic response of the canine hairs to immunological stress, i.e., the ionomic profiles of canine hairs is strongly affected by the stress induced by LPS injections.
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Affiliation(s)
- Kyoung-Min So
- Animal Nutrition and Physiology Team, National Institute of Animal Science, RDA, Wanju, 55365, South Korea
| | - Yoonseok Lee
- Institute of Green-Bio Science and Technology, Seoul National University, 1447 Pyungchang-daero, Pyungchang, 25354, Republic of Korea
| | - Jin Duck Bok
- Institute of Green-Bio Science and Technology, Seoul National University, 1447 Pyungchang-daero, Pyungchang, 25354, Republic of Korea
| | - Eun Bae Kim
- Department of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
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30
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Han GG, Kim EB, Lee J, Lee JY, Jin G, Park J, Huh CS, Kwon IK, Kil DY, Choi YJ, Kong C. Relationship between the microbiota in different sections of the gastrointestinal tract, and the body weight of broiler chickens. Springerplus 2016; 5:911. [PMID: 27386355 PMCID: PMC4927549 DOI: 10.1186/s40064-016-2604-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 06/16/2016] [Indexed: 02/07/2023]
Abstract
In the poultry industry, many efforts have been undertaken to further improve the growth performance of broilers and identification and modulation of body weight (BW)-related bacteria could be one of the strategies to improve productivity. However, studies regarding the relationship between microbiota and BW are scarce. The objective of the present study was to investigate the relationship between microbiota and BW in different sections of the gastrointestinal tract (GIT). A total of twenty 18-day-old birds were selected based on the BW, and samples were collected from the three different sections of the GIT, which included the crop, ileum and cecum. Bacterial genomic DNA was extracted from the samples, and the V4 region of 16S rRNA gene were amplified. Amplicons were sequenced on Illumina MiSeq, and microbial communities were analyzed by using QIIME. In principal coordinate analysis, bacterial communities were clustered into three groups, based on the sections of GIT. Several BW-related bacterial groups were identified from linear regression analysis. At the genus level, Streptococcus from the ileum as well as Akkermansia in both ileum and cecum, were negatively related to BW, whereas Bifidobacterium in the ileum and Lactococcus in the cecum showed a positive correlation. The results from the present study showed that particular bacterial communities in the GIT were related to BW, and the study has broadened the understanding of the intestinal microbial ecosystem in broiler chickens.
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Affiliation(s)
- Geon Goo Han
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Eun Bae Kim
- Department of Animal Life Science, Kangwon National University, Chuncheon, Gangwon-do Republic of Korea.,Division of Applied Animal Science, Kangwon National University, Chuncheon, Gangwon-do Republic of Korea
| | - Jinyoung Lee
- Department of Animal Science and Technology, Konkuk University, Seoul, Republic of Korea
| | - Jun-Yeong Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Gwideuk Jin
- Department of Animal Life Science, Kangwon National University, Chuncheon, Gangwon-do Republic of Korea
| | - Jongbin Park
- Department of Animal Life System, Kangwon National University, Chuncheon, Gangwon-do Republic of Korea
| | - Chul-Sung Huh
- Institute of Green-Bio Science and Technology, Seoul National University, Pyeongchang, Gangwon-do Republic of Korea
| | - Ill-Kyong Kwon
- Department of Animal Life Science, Kangwon National University, Chuncheon, Gangwon-do Republic of Korea
| | - Dong Yong Kil
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do Republic of Korea
| | - Yun-Jaie Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea.,Research Institute for Agriculture and Life Science, Seoul National University, Seoul, Republic of Korea
| | - Changsu Kong
- Department of Animal Science and Technology, Konkuk University, Seoul, Republic of Korea
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31
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Kim EB, Jin GD, Lee JY, Choi YJ. Genomic Features and Niche-Adaptation of Enterococcus faecium Strains from Korean Soybean-Fermented Foods. PLoS One 2016; 11:e0153279. [PMID: 27070419 PMCID: PMC4829236 DOI: 10.1371/journal.pone.0153279] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/25/2016] [Indexed: 01/19/2023] Open
Abstract
Certain strains of Enterococcus faecium contribute beneficially to human health and food fermentation. However, other E. faecium strains are opportunistic pathogens due to the acquisition of virulence factors and antibiotic resistance determinants. To characterize E. faecium from soybean fermentation, we sequenced the genomes of 10 E. faecium strains from Korean soybean-fermented foods and analyzed their genomes by comparing them with 51 clinical and 52 non-clinical strains of different origins. Hierarchical clustering based on 13,820 orthologous genes from all E. faecium genomes showed that the 10 strains are distinguished from most of the clinical strains. Like non-clinical strains, their genomes are significantly smaller than clinical strains due to fewer accessory genes associated with antibiotic resistance, virulence, and mobile genetic elements. Moreover, we identified niche-associated gene gain and loss from the soybean strains. Thus, we conclude that soybean E. faecium strains might have evolved to have distinctive genomic features that may contribute to its ability to thrive during soybean fermentation.
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Affiliation(s)
- Eun Bae Kim
- Department of Animal Life Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea
- Division of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea
| | - Gwi-Deuk Jin
- Department of Animal Life Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea
| | - Jun-Yeong Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Yun-Jaie Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
- Research Institute for Agriculture and Life Science, Seoul National University, Seoul, Republic of Korea
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32
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Cooper D, Kim EB, Marco M, Rust B, Welch L, Horn W, Martin R, Keim N. Relationship between Human Gut Microbiota and Interleukin 6 Levels in Overweight and Obese Adults. FASEB J 2016. [DOI: 10.1096/fasebj.30.1_supplement.146.4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Eun Bae Kim
- UC DavisDavisCA
- Seoul National UniversityGwanak‐guSeoulRepublic of Korea
| | | | - Bret Rust
- UC DavisDavisCA
- WHNRC ARS USDADavisCA
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33
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Hwang JY, Lee SG, Kim EB. Polymorphic sites in complete genome sequences of Asian badger, Meles leucurus amurensis (Mustelidae, Melinae) mitochondria. Mitochondrial DNA B Resour 2016; 1:264-265. [PMID: 33644355 PMCID: PMC7871861 DOI: 10.1080/23802359.2016.1159932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The badger is a common carnivorous animal maintain ecosystem by regulating the population of their prey. However, genomic information such as sequence polymorphisms has been restricted until recently. In this study, we have sequenced and assembled complete mitogenomes of Asian badgers, Meles leucurus amurensis, and polymorphic sites were identified. A total 182 singleton polymorphic sites were identified, and the 92 sites were located in protein-coding genes. Phylogenetic analysis showed that Asian badgers are evolutionary closed to Japanese badgers rather than European badgers. This study will provide important genomic information to assign taxon of species and to identify species of mustelids.
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Affiliation(s)
- Jae Yeon Hwang
- Department of Animal Life Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Eun Bae Kim
- Department of Animal Life Science, Kangwon National University, Chuncheon, Republic of Korea
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Kim KH, Arokiyaraj S, Lee J, Oh YK, Chung HY, Jin GD, Kim EB, Kim EK, Lee Y, Baik M. Effect of rhubarb (Rheum spp.) root on in vitro and in vivo ruminal methane production and a bacterial community analysis based on 16S rRNA sequence. Anim Prod Sci 2016. [DOI: 10.1071/an15585] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The objective of this study was to evaluate the anti-methanogenic effect of rhubarb (Rheum spp.) on in vitro, in vivo, and bacterial community composition using Quantitative Insights into Microbial Ecology sequencing. Rhubarb root powder was tested at different concentrations (0, 0.33, 0.67, and 1.33 g/L) in vitro, and all incubations were carried out in triplicate two runs on separate days. Concentrations of 0.67 and 1.33 g/L rhubarb significantly (P < 0.05) reduced methane production and the acetate : propionate ratio compared with those of the Control, without adverse effects on total volatile fatty acids and total gas production. In the second in vivo trial, four Hanwoo (Korean native) steers (live bodyweight, 556 ± 46 kg) with a ruminal cannula were housed individually in metabolic stalls and fed a basal diet twice daily in equal amounts at 0900 hours and 2100 hours. The before rhubarb treatment (before treatment) duration was 24 days for all steers; 14 days were used for diet adaptation and 10 days were used for gas samples collected 1, 2, and 3 h after the morning feeding on Days 3, 5, 7, and 9. We used three syringe needles passed through the ruminal cannula stopper at different time points as a simple and rapid method to sample rumen gas. Thereafter, three mesh bags containing 30 g of sliced rhubarb root each were placed at different depths in the rumen of each steer for 14 days (after treatment), and gas samples were collected on Days 4, 7, 10, 12, and 13. The results showed a significant (P < 0.05) decrease in methane concentration from the rhubarb-treated steers and provide the evidence that this method would be useful for in vivo screening of anti-methanogenic feed additives or plant material. Furthermore, 16s RNA sequencing after treatment showed increases in the numbers of Prevotella, and Lactobacillus, but decreases in Methanobrevibacter. In conclusion, rhubarb had an anti-methanogenic effect in vitro and in vivo, and the increase in the number of Prevotella shifted ruminal fermentation towards propionate production.
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35
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Lee JY, Kang SK, Heo YJ, Shin DW, Park TE, Han GG, Jin GD, Lee HB, Jung E, Kim HS, Na Y, Kim EB, Choi YJ. Influence of Flaxseed Oil on Fecal Microbiota, Egg Quality and Fatty Acid Composition of Egg Yolks in Laying Hens. Curr Microbiol 2015; 72:259-66. [PMID: 26613617 DOI: 10.1007/s00284-015-0946-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 10/16/2015] [Indexed: 12/18/2022]
Abstract
Although there have been many attempts to produce ω-3 fatty acid-rich eggs using alpha-linolenic acid (ALA) that is a popular fatty acid in the poultry feed industry, only limited knowledge about the effects of ALA-enriched diets on chicken fecal microbiota is currently available. Herein we examined the changes in the fecal microbiota composition, egg quality traits and fatty acid composition of the egg yolks of laying hens fed ALA-rich flaxseed oil for 8 weeks. The animals fed the experimental diets that contained 0 % (group C), 0.5 % (group T1), and 1.0 % (group T2) of flaxseed oil, respectively, and eggs and feces were obtained for the analyses. ω-3 fatty acids, including ALA, were increased in T1 and T2 compared with C. Furthermore, the freshness of eggs was improved with no side effects on the eggs. The diet also changed the fecal microbiota; Firmicutes was increased in T1 and T2 (48.6 to 83 and 79.6 %) and Bacteroidetes was decreased (40.2 to 8.8 and 4.2 %). Principal coordinate analysis revealed that Lactobacillus, among the 56 examined genera, was the most influenced bacterial group in terms of the fecal microbial community shifts. These results indicate that ALA-rich diets influenced both the egg and fecal microbiota in beneficial manners in laying hens although the association between the fatty acid composition of the egg yolk and the fecal microbiota was not clear. This study is a first step to understand the effect of flaxseed oil as well as intestinal microbiota of laying hens.
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Affiliation(s)
- Jun-Yeong Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Sang-Kee Kang
- Institute of Green-Bio Science & Technology, Seoul National University, Pyeongchang, Gangwon-do, Republic of Korea
| | - Yun-Jeong Heo
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Do-Woon Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Tae-Eun Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Geon Goo Han
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Gwi-Deuk Jin
- Department of Animal Life Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Ho-Bin Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Eojin Jung
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Hee Sung Kim
- SeoulFeed Company, Limited, Incheon, Republic of Korea
| | - Yerim Na
- SPC Research Institute of Food and Biotechnology, Seoul, Republic of Korea
| | - Eun Bae Kim
- Department of Animal Life Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea.
| | - Yun-Jaie Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea. .,Research Institute for Agriculture and Life Science, Seoul National University, Seoul, Republic of Korea.
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Ma S, Lee SG, Kim EB, Park TJ, Seluanov A, Gorbunova V, Buffenstein R, Seravalli J, Gladyshev VN. Organization of the Mammalian Ionome According to Organ Origin, Lineage Specialization, and Longevity. Cell Rep 2015; 13:1319-1326. [PMID: 26549444 DOI: 10.1016/j.celrep.2015.10.014] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 08/19/2015] [Accepted: 10/05/2015] [Indexed: 12/16/2022] Open
Abstract
Trace elements are essential to all mammals, but their distribution and utilization across species and organs remains unclear. Here, we examined 18 elements in the brain, heart, kidney, and liver of 26 mammalian species and report the elemental composition of these organs, the patterns of utilization across the species, and their correlation with body mass and longevity. Across the organs, we observed distinct distribution patterns for abundant elements, transition metals, and toxic elements. Some elements showed lineage-specific patterns, including reduced selenium utilization in African mole rats, and positive correlation between the number of selenocysteine residues in selenoprotein P and the selenium levels in liver and kidney across mammals. Body mass was linked positively to zinc levels, whereas species lifespan correlated positively with cadmium and negatively with selenium. This study provides insights into the variation of mammalian ionome by organ physiology, lineage specialization, body mass, and longevity.
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Affiliation(s)
- Siming Ma
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Bioinspired Science, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Eun Bae Kim
- Department of Bioinspired Science, Ewha Womans University, Seoul 120-750, Republic of Korea; Department of Animal Life Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, Kangwon-do 200-701, Republic of Korea
| | - Thomas J Park
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Rochelle Buffenstein
- Department of Physiology and The Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center, San Antonio, TX 78245, USA
| | - Javier Seravalli
- Redox Biology Center and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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Hwang JY, Lee CK, Kim H, Nam BH, An CM, Park JY, Park KH, Huh CS, Kim EB. Comparative genomic analysis of mitochondrial protein-coding genes in Veneroida clams: Analysis of superfamily-specific genomic and evolutionary features. Mar Genomics 2015; 24 Pt 3:329-34. [PMID: 26343338 DOI: 10.1016/j.margen.2015.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 08/19/2015] [Accepted: 08/19/2015] [Indexed: 12/30/2022]
Abstract
Veneroida is the largest order of bivalves, and these clams are commercially important in Asian countries. Although numerous studies have focused on the genomic characters of individual species or genera in Veneroida, superfamily-specific genomic characters have not been determined. In this study, we performed a comparative genomic analysis of 12 mitochondrial protein coding genes (PCGs) from 25 clams in six Veneroida superfamilies to determine genomic and evolutionary features of each superfamily. Length and distribution of nucleotides encoding the PCGs were too variable to define superfamily-specific genomic characters. Phylogenetic analysis revealed that PCGs are suitable for classification of species in three superfamilies: Cardioidea, Mactroidea, and Veneroidea. However, one species classified in Tellinoidea, Sinonovacula constricta, was evolutionarily closer to Solenoidea clams than Tellinoidea clams. dN/dS analysis showed that positively selected sites in NADH dehydrogenase subunit, nd4 and subunit of ATP synthase, atp6 were present in Mactroidea. Differences in selected sites in the nd4 and atp6 could be caused by superfamily-level differences in sodium transport or ATP synthesis functions, respectively. These differences in selected sites in NADH may have conferred these animals, which have low motility and do not generally move, with increased flexibility to maintain homeostasis in the face of osmotic pressure. Our study provides insight into evolutionary traits as well as facilitates identification of veneroids.
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Affiliation(s)
- Jae Yeon Hwang
- Department of Animal Life Science, Kangwon National University, Chuncheon 200-701, Republic of Korea
| | - Chang-Kyu Lee
- Department of Agricultural Biotechnology, Animal Biotechnology Major, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921 Republic of Korea; Institute of Green Bio Science and Technology, Seoul National University, Kangwon-do 232-916, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology, Animal Biotechnology Major, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921 Republic of Korea; Institute of Green Bio Science and Technology, Seoul National University, Kangwon-do 232-916, Republic of Korea
| | - Bo-Hye Nam
- Biotechnology Research Division, National Fisheries Research and Development Institute, Busan 619-705, Republic of Korea
| | - Cheul Min An
- Biotechnology Research Division, National Fisheries Research and Development Institute, Busan 619-705, Republic of Korea
| | - Jung Youn Park
- Biotechnology Research Division, National Fisheries Research and Development Institute, Busan 619-705, Republic of Korea
| | - Kyu-Hyun Park
- Department of Animal Life System, Kangwon National University, Chuncheon 200-701, Republic of Korea
| | - Chul-Sung Huh
- Graduate School of International Agricultural Technology/GBST, Seoul National University, Pyeongchang 232-916, Republic of Korea
| | - Eun Bae Kim
- Department of Animal Life Science, Kangwon National University, Chuncheon 200-701, Republic of Korea.
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Hwang JY, Jin GD, Park J, Lee SG, Kim EB. Complete sequences of eastern water bat, Myotis petax (Chiroptera; Microchiroptera; Vespertilionidae) mitogenome. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3715-6. [DOI: 10.3109/19401736.2015.1079871] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
| | | | - Jongbin Park
- Department of Animal Life System, Kangwon National University, Chuncheon, Republic of Korea, and
| | - Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
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Hwang JY, Choi KH, Lee DK, Kim SH, Kim EB, Hyun SH, Lee CK. Overexpression of OCT4A ortholog elevates endogenous XIST in porcine parthenogenic blastocysts. J Reprod Dev 2015; 61:533-40. [PMID: 26255835 PMCID: PMC4685219 DOI: 10.1262/jrd.2015-017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
X-chromosome inactivation (XCI) is an epigenetic process that equalizes expression of X-borne genes between
male and female eutherians. This process is observed in early eutherian embryo development in a
species-specific manner. Until recently, various pluripotent factors have been suggested to regulate the
process of XCI by repressing XIST expression, which is the master inducer for XCI. Recent
insights into the process and its regulation have been restricted in mouse species despite the evolutionary
diversity of the process and molecular mechanism among the species. OCT4A is one of the
represented pluripotent factors, the gate-keeper for maintaining pluripotency, and an XIST
repressor. Therefore, in here, we examined the relation between OCT4A and X-linked genes in
porcine preimplantation embryos. Three X-linked genes, XIST,
LOC102165544, and RLIM, were selected in present study because their
orthologues have been known to regulate XCI in mice. Expression levels of OCT4A were
positively correlated with XIST and LOC102165544 in female blastocysts.
Furthermore, overexpression of exogenous human OCT4A in cleaved parthenotes generated
blastocysts with increased XIST expression levels. However, increased XIST
expression was not observed when exogenous OCT4A was obtained from early blastocysts. These
results suggest the possibility that OCT4A would be directly or indirectly involved in
XIST expression in earlier stage porcine embryos rather than blastocysts.
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Affiliation(s)
- Jae Yeon Hwang
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
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Hwang JY, Han GG, Park JY, Kim EM, An CM, Kang JH, Choi YJ, Kim EB. Complete sequence and polymorphisms of female Ruditapes philippinarum (Mollusca: Bivalvia) mitochondria genome. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3462-3. [PMID: 26248000 DOI: 10.3109/19401736.2015.1066348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mitogenome of female Ruditapes philippinarum organism was sequenced, and genomic variation and phylogeny were examined in this study. Length of the mitogenome was 22 089 bp showing 94.28% of sequence identity with previously reported sequence. Total 707 single nucleotide polymorphisms, SNPs, were detected and 50 residues were non-synonymous SNPs among the 202 SNPs in protein-coding genes. Deleted genomic fragments with of 265 bp and 322 bp were observed in non-coding regions, ND2 to ND4L and ND4L to tRNA(Ile), respectively. Phylogenic analysis confirmed that used organisms were female R. philippinarum, and the species has closer evolutionary distance with genus Paphia rather than genus Meretrix. Our finding will be help to set an insight for population and evolutionary genomics of Veneroida clams as well as application to marine industry.
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Affiliation(s)
- Jae Yeon Hwang
- a Department of Animal Life Science , Kangwon National University , Chuncheon , Republic of Korea
| | - Geon Goo Han
- b Department of Agricultural Biotechnology , Seoul National University , Seoul , Republic of Korea
| | - Jung Youn Park
- c Biotechnology Research Division , National Fisheries Research and Development Institute , Busan , Korea , and
| | - Eun-Mi Kim
- c Biotechnology Research Division , National Fisheries Research and Development Institute , Busan , Korea , and
| | - Cheul Min An
- c Biotechnology Research Division , National Fisheries Research and Development Institute , Busan , Korea , and
| | - Jung-Ha Kang
- c Biotechnology Research Division , National Fisheries Research and Development Institute , Busan , Korea , and
| | - Yun-Jaie Choi
- b Department of Agricultural Biotechnology , Seoul National University , Seoul , Republic of Korea .,d Research Institute for Agriculture and Life Science, Seoul National University , Seoul , Republic of Korea
| | - Eun Bae Kim
- a Department of Animal Life Science , Kangwon National University , Chuncheon , Republic of Korea
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41
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Ma S, Yim SH, Lee SG, Kim EB, Lee SR, Chang KT, Buffenstein R, Lewis KN, Park TJ, Miller RA, Clish CB, Gladyshev VN. Organization of the Mammalian Metabolome according to Organ Function, Lineage Specialization, and Longevity. Cell Metab 2015; 22:332-43. [PMID: 26244935 PMCID: PMC4758382 DOI: 10.1016/j.cmet.2015.07.005] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 04/15/2015] [Accepted: 07/02/2015] [Indexed: 12/24/2022]
Abstract
Biological diversity among mammals is remarkable. Mammalian body weights range seven orders of magnitude and lifespans differ more than 100-fold among species. While genetic, dietary, and pharmacological interventions can be used to modulate these traits in model organisms, it is unknown how they are determined by natural selection. By profiling metabolites in brain, heart, kidney, and liver tissues of 26 mammalian species representing ten taxonomical orders, we report metabolite patterns characteristic of organs, lineages, and species longevity. Our data suggest different rates of metabolite divergence across organs and reveal patterns representing organ-specific functions and lineage-specific physiologies. We identified metabolites that correlated with species lifespan, some of which were previously implicated in longevity control. We also compared the results with metabolite changes in five long-lived mouse models and observed some similar patterns. Overall, this study describes adjustments of the mammalian metabolome according to lifespan, phylogeny, and organ and lineage specialization.
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Affiliation(s)
- Siming Ma
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sun Hee Yim
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA.
| | - Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Bioinspired Science, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Eun Bae Kim
- Department of Bioinspired Science, Ewha Womans University, Seoul 120-750, Republic of Korea; Department of Animal Life Science, Kangwon National University, Chuncheon 200-701, Republic of Korea
| | - Sang-Rae Lee
- The National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Cheongwon, Chungbuk 363-883, Republic of Korea
| | - Kyu-Tae Chang
- The National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Cheongwon, Chungbuk 363-883, Republic of Korea
| | - Rochelle Buffenstein
- Department of Physiology and The Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center, San Antonio, TX 78245, USA
| | - Kaitlyn N Lewis
- Department of Physiology and The Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center, San Antonio, TX 78245, USA
| | - Thomas J Park
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Richard A Miller
- Department of Pathology and Geriatrics Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA.
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Hwang JY, Jin GD, Park J, Kim H, Lee CK, Kwak W, Nam BH, An CM, Park JY, Park KH, Huh CS, Kim EB. Complete genome sequence and SNPs of Raja pulchra (Rajiformes, Rajidae) mitochondria. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2975-7. [PMID: 26122344 DOI: 10.3109/19401736.2015.1060467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mitochondrial genomes were sequenced from five Raja pulchra individuals, and single-nucleotide polymorphisms (SNPs) were identified by comparing previously announced sequences in this study. Total 117 SNPs were detected and they were present in 2 rRNA genes, 9 tRNA genes, 13 protein coding genes and non-coding region. One deleted polymorphic site, which was located in 16S rRNA gene, was observed in two individuals. Six polymorphic sites were non-synonymous SNPs, which were distributed in ND1, ND2, ATP6 and ND4 gene. Phylogenic analysis validated current taxa. The genome sequences of R. pulchra mitochondria could be comparable information for understanding species divergence and genomic variation among the populations.
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Affiliation(s)
| | | | - Jongbin Park
- b Department of Animal Life System , Kangwon National University , Chuncheon , Republic of Korea
| | - Heebal Kim
- c Department of Agricultural Biotechnology , Animal Biotechnology Major, Research Institute for Agriculture and Life Sciences, Seoul National University , Seoul , Republic of Korea .,d Institute of Green Bio Science and Technology, Seoul National University , Pyeongchang , Republic of Korea
| | - Chang-Kyu Lee
- c Department of Agricultural Biotechnology , Animal Biotechnology Major, Research Institute for Agriculture and Life Sciences, Seoul National University , Seoul , Republic of Korea .,d Institute of Green Bio Science and Technology, Seoul National University , Pyeongchang , Republic of Korea
| | - Woori Kwak
- c Department of Agricultural Biotechnology , Animal Biotechnology Major, Research Institute for Agriculture and Life Sciences, Seoul National University , Seoul , Republic of Korea .,e C&K Genomics, Seoul National University Research Park , Seoul , Republic of Korea
| | - Bo-Hye Nam
- f Biotechnology Research Division , National Fisheries Research & Development Institute , Busan , Republic of Korea , and
| | - Cheul Min An
- f Biotechnology Research Division , National Fisheries Research & Development Institute , Busan , Republic of Korea , and
| | - Jung Youn Park
- f Biotechnology Research Division , National Fisheries Research & Development Institute , Busan , Republic of Korea , and
| | - Kyu-Hyun Park
- b Department of Animal Life System , Kangwon National University , Chuncheon , Republic of Korea
| | - Chul-Sung Huh
- g Graduate School of International Agricultural Technology/GBST, Seoul National University , Pyeongchang , Republic of Korea
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Fushan AA, Turanov AA, Lee S, Kim EB, Lobanov AV, Yim SH, Buffenstein R, Lee S, Chang K, Rhee H, Kim J, Yang K, Gladyshev VN. Gene expression defines natural changes in mammalian lifespan. Aging Cell 2015; 14:352-65. [PMID: 25677554 PMCID: PMC4406664 DOI: 10.1111/acel.12283] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2014] [Indexed: 01/09/2023] Open
Abstract
Mammals differ more than 100-fold in maximum lifespan, which can be altered in either direction during evolution, but the molecular basis for natural changes in longevity is not understood. Divergent evolution of mammals also led to extensive changes in gene expression within and between lineages. To understand the relationship between lifespan and variation in gene expression, we carried out RNA-seq-based gene expression analyses of liver, kidney, and brain of 33 diverse species of mammals. Our analysis uncovered parallel evolution of gene expression and lifespan, as well as the associated life-history traits, and identified the processes and pathways involved. These findings provide direct insights into how nature reversibly adjusts lifespan and other traits during adaptive radiation of lineages.
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Affiliation(s)
- Alexey A. Fushan
- Department of Bioinspired Science Ewha Womans University Seoul 120‐750South Korea
| | - Anton A. Turanov
- Division of Genetics Department of Medicine Brigham and Women's Hospital Harvard Medical School Boston MA 02115USA
| | - Sang‐Goo Lee
- Department of Bioinspired Science Ewha Womans University Seoul 120‐750South Korea
- Division of Genetics Department of Medicine Brigham and Women's Hospital Harvard Medical School Boston MA 02115USA
| | - Eun Bae Kim
- Department of Bioinspired Science Ewha Womans University Seoul 120‐750South Korea
- Department of Animal Life Science Kangwon National University Chuncheon 200‐701South Korea
| | - Alexei V. Lobanov
- Division of Genetics Department of Medicine Brigham and Women's Hospital Harvard Medical School Boston MA 02115USA
| | - Sun Hee Yim
- Division of Genetics Department of Medicine Brigham and Women's Hospital Harvard Medical School Boston MA 02115USA
| | - Rochelle Buffenstein
- Department of Physiology and The Sam and Ann Barshop Institute for Longevity and Aging Studies University of Texas Health Science Center San Antonio TX 78245USA
| | - Sang‐Rae Lee
- The National Primate Research Center Korea Research Institute of Bioscience and Biotechnology OchangCheongwon Chungbuk 363‐883 South Korea
| | - Kyu‐Tae Chang
- The National Primate Research Center Korea Research Institute of Bioscience and Biotechnology OchangCheongwon Chungbuk 363‐883 South Korea
| | | | - Jong‐So Kim
- Macrogene, Inc. Geumchen‐guSeoul 153‐781South Korea
| | | | - Vadim N. Gladyshev
- Department of Bioinspired Science Ewha Womans University Seoul 120‐750South Korea
- Division of Genetics Department of Medicine Brigham and Women's Hospital Harvard Medical School Boston MA 02115USA
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44
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Fang X, Seim I, Huang Z, Gerashchenko MV, Xiong Z, Turanov AA, Zhu Y, Lobanov AV, Fan D, Yim SH, Yao X, Ma S, Yang L, Lee SG, Kim EB, Bronson RT, Šumbera R, Buffenstein R, Zhou X, Krogh A, Park TJ, Zhang G, Wang J, Gladyshev VN. Adaptations to a subterranean environment and longevity revealed by the analysis of mole rat genomes. Cell Rep 2014; 8:1354-64. [PMID: 25176646 PMCID: PMC4350764 DOI: 10.1016/j.celrep.2014.07.030] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 05/11/2014] [Accepted: 07/17/2014] [Indexed: 02/06/2023] Open
Abstract
Subterranean mammals spend their lives in dark, unventilated environments that are rich in carbon dioxide and ammonia and low in oxygen. Many of these animals are also long-lived and exhibit reduced aging-associated diseases, such as neurodegenerative disorders and cancer. We sequenced the genome of the Damaraland mole rat (DMR, Fukomys damarensis) and improved the genome assembly of the naked mole rat (NMR, Heterocephalus glaber). Comparative genome analyses, along with the transcriptomes of related subterranean rodents, revealed candidate molecular adaptations for subterranean life and longevity, including a divergent insulin peptide, expression of oxygen-carrying globins in the brain, prevention of high CO2-induced pain perception, and enhanced ammonia detoxification. Juxtaposition of the genomes of DMR and other more conventional animals with the genome of NMR revealed several truly exceptional NMR features: unusual thermogenesis, an aberrant melatonin system, pain insensitivity, and unique processing of 28S rRNA. Together, these genomes and transcriptomes extend our understanding of subterranean adaptations, stress resistance, and longevity.
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Affiliation(s)
- Xiaodong Fang
- BGI-Shenzhen, Shenzhen 518083, China; Department of Biology, University of Copenhagen, Copenhagen, 2200 Copenhagen N, Denmark
| | - Inge Seim
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Bioinspired Science, Ewha Womans University, Seoul 120-750, South Korea
| | | | - Maxim V Gerashchenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Anton A Turanov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Alexei V Lobanov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Sun Hee Yim
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Siming Ma
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Lan Yang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Bioinspired Science, Ewha Womans University, Seoul 120-750, South Korea
| | - Eun Bae Kim
- Department of Bioinspired Science, Ewha Womans University, Seoul 120-750, South Korea
| | - Roderick T Bronson
- Rodent Histopathology Laboratory, Harvard Medical School, Boston, MA 02115, USA
| | - Radim Šumbera
- University of South Bohemia, Faculty of Science, Ceske Budejovice 37005, Czech Republic
| | - Rochelle Buffenstein
- Department of Physiology and The Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center, San Antonio, TX 78245, USA
| | - Xin Zhou
- BGI-Shenzhen, Shenzhen 518083, China
| | - Anders Krogh
- Department of Biology, University of Copenhagen, Copenhagen, 2200 Copenhagen N, Denmark
| | - Thomas J Park
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Guojie Zhang
- BGI-Shenzhen, Shenzhen 518083, China; Department of Biology, University of Copenhagen, Copenhagen, 2200 Copenhagen N, Denmark
| | - Jun Wang
- BGI-Shenzhen, Shenzhen 518083, China; Department of Biology, University of Copenhagen, Copenhagen, 2200 Copenhagen N, Denmark; King Abdulaziz University, Jeddah 21441, Saudi Arabia.
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Bioinspired Science, Ewha Womans University, Seoul 120-750, South Korea.
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45
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Kim EB, Lee SG. The complete mitochondrial genome of the Mongolian gerbil, Meriones unguiculatus (Rodentia: Muridae: Gerbillinae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1457-8. [PMID: 25185794 DOI: 10.3109/19401736.2014.953091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of the Mongolian gerbil, Meriones unguiculatus, was sequenced. The 16,360 bp long genome has 37 genes typical for rodent mitogenomes, including 22 tRNA genes, 2 rRNA genes, and 13 protein-coding genes. The total GC content of the mitochondrial genome is 36.96% with the base composition of 32.61% A, 23.71% C, 13.24% G, and 30.44% T. Translational terminators of three genes (cytb, cox3, and nad4) were generated by the addition of 3' A residues to the mRNA. This novel rodent mitochondrial genome will provide comparable information for understanding the rodent mitochondrial evolution.
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Affiliation(s)
- Eun Bae Kim
- a Department of Bioinspired Science , Ewha Womans University , Seoul , Republic of Korea .,b Department of Animal Life Science , Kangwon National University , Chuncheon , Republic of Korea , and
| | - Sang-Goo Lee
- a Department of Bioinspired Science , Ewha Womans University , Seoul , Republic of Korea .,c Division of Genetics, Department of Medicine , Brigham and Women's Hospital, Harvard Medical School , Boston , MA 02115 , USA
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46
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Rust B, Horn W, Cooper D, Welch L, Martin R, Pelkman C, Kim EB, Marco M, Keim N. Does production of methane in the gut affect glucose tolerance? (822.10). FASEB J 2014. [DOI: 10.1096/fasebj.28.1_supplement.822.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Bret Rust
- Nutrition UC DavisDavisCAUnited States
- USDA / ARS / Western Human Nutrition Research CenterDavisCAUnited States
| | - William Horn
- USDA / ARS / Western Human Nutrition Research CenterDavisCAUnited States
| | | | - Lucas Welch
- USDA / ARS / Western Human Nutrition Research CenterDavisCAUnited States
| | | | | | | | | | - Nancy Keim
- Nutrition UC DavisDavisCAUnited States
- USDA / ARS / Western Human Nutrition Research CenterDavisCAUnited States
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Yin X, Yan Y, Kim EB, Lee B, Marco ML. Short communication: effect of milk and milk containing Lactobacillus casei on the intestinal microbiota of mice. J Dairy Sci 2014; 97:2049-55. [PMID: 24508432 DOI: 10.3168/jds.2013-7477] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 12/24/2013] [Indexed: 12/18/2022]
Abstract
BALB/c mice were fed milk or Lactobacillus casei BL23 in milk for 14d and fecal samples were collected at d 0, 4, and 7 as well as 1 and 8d after the last administration. According to high-throughput DNA sequencing of the 16S rRNA genes extracted from the fecal microbiota, the bacterial diversity in the fecal samples of all mice increased over time. After 14d of administration, the consumption of milk and milk containing L. casei BL23 resulted in distinct effects on the microbial composition in the intestine. Specifically, the proportions of bacteria in the Lactobacillaceae, Porphyromonadaceae, and Comamonadaceae were significantly higher in mice fed the L. casei BL23-milk culture compared with one or more of the other groups of mice. The relative amounts of Lachnospiraceae were higher and Streptococcaceae were lower in mice fed milk alone. The changes were not found at d 4 and 7 during milk and L. casei feeding and were no longer detected 8d after administration was stopped. This study shows that consumption of milk or probiotic L. casei-containing milk results in non-overlapping, taxa-specific effects on the bacteria in the distal murine intestine.
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Affiliation(s)
- Xiaochen Yin
- Department of Food Science & Technology, University of California, Davis 95616
| | - Yinzhuo Yan
- Department of Food Science & Technology, University of California, Davis 95616
| | - Eun Bae Kim
- Department of Food Science & Technology, University of California, Davis 95616
| | - Bokyung Lee
- Department of Food Science & Technology, University of California, Davis 95616
| | - Maria L Marco
- Department of Food Science & Technology, University of California, Davis 95616.
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Hwang JY, Kim EB, Ka H, Lee CK. Identification of the porcine XIST gene and its differential CpG methylation status in male and female pig cells. PLoS One 2013; 8:e73677. [PMID: 24040022 PMCID: PMC3767593 DOI: 10.1371/journal.pone.0073677] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 07/22/2013] [Indexed: 11/18/2022] Open
Abstract
XIST, a long non-coding RNA, plays an important role in triggering X chromosome inactivation in eutherians, and is used extensively for qualifying stem cells and cloned embryos. However, a porcine XIST has not yet been thoroughly identified despite its biological importance in a wide variety of research fields. Here, we present a full-length porcine XIST sequence assembled using known sequences (GenBank), RNA-Seq data (NCBI SRA), and PCR/sequencing. The proposed porcine XIST gene model encodes a 25,215-bp transcript consisting of 7 exons, including two conserved and two porcine-specific repeat regions. Transcription covering the entire XIST region was observed specifically in female cells, but not in male cells. We also identified eight transcription starting sites (TSSs) and evaluated CpG methylation patterns in the upstream (+2.0 kb) and downstream (−2.0 kb) regions. Sixty-seven CG di-nucleotides identified in the target region were considered to be candidate CpG sites, and were enriched in the following two regions: −284 to +53 bp (13 sites) and +285 to +1,727 bp (54 sites) from the selected TSS. Male 5` region of XIST (64.5 sites, 96.26%) had a higher level of CpG methylation than female DNA (33.4 sites, 49.85%). Taken together, our results revealed that the porcine XIST gene is expressed exclusively in female cells, which is influenced by the lower level of CpG methylation in the putative promoter region compared with male cells. The porcine XIST presented in this study represents a useful tool for related research areas such as porcine embryology and stem cell biology.
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Affiliation(s)
- Jae Yeon Hwang
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Eun Bae Kim
- Department of Food Science and Technology, University of California, Davis, California, United States of America
- Department of Animal Products and Food Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea
| | - Hakhyun Ka
- Division of Biological Science and Technology, Institute of Biomaterials and Institute for Poverty Alleviation and International Development, Yonsei University, Wonju, Kangwon-do, Republic of Korea
| | - Chang-Kyu Lee
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- * E-mail:
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Kim EB, Fang X, Fushan AA, Huang Z, Lobanov AV, Han L, Marino SM, Sun X, Turanov AA, Yang P, Yim SH, Zhao X, Kasaikina MV, Stoletzki N, Peng C, Polak P, Xiong Z, Kiezun A, Zhu Y, Chen Y, Kryukov GV, Zhang Q, Peshkin L, Yang L, Bronson RT, Buffenstein R, Wang B, Han C, Li Q, Chen L, Zhao W, Sunyaev SR, Park TJ, Zhang G, Wang J, Gladyshev VN. Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature 2011; 479:223-7. [PMID: 21993625 PMCID: PMC3319411 DOI: 10.1038/nature10533] [Citation(s) in RCA: 412] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 09/05/2011] [Indexed: 11/15/2022]
Abstract
The naked mole rat (NMR, Heterocephalus glaber) is a strictly subterranean, extraordinarily long-lived eusocial mammal1. Although the size of a mouse, its maximum lifespan exceeds 30 years and makes this animal the longest living rodent. NMRs show negligible senescence, no age-related increase in mortality, and high fecundity until death2. In addition to delayed aging, NMRs are resistant to both spontaneous cancer and experimentally induced tumorigenesis3,4. NMRs pose a challenge to the theories that link aging, cancer and redox homeostasis. Although characterized by significant oxidative stress5, the NMR proteome does not show age-related susceptibility to oxidative damage nor increased ubiquitination6. NMRs naturally reside in large colonies with a single breeding female, the “queen,” who suppresses the sexual maturity of her subordinates11. NMRs also live in full darkness, at low oxygen and high carbon dioxide concentrations7, and are unable to sustain thermogenesis8 nor feel certain types of pain9,10. Here we report sequencing and analysis of the NMR genome, which revealed unique genome features and molecular adaptations consistent with cancer resistance, poikilothermy, hairlessness, altered visual function, circadian rhythms and taste sensing, and insensitivity to low oxygen. This information provides insights into NMR’s exceptional longevity and capabilities to live in hostile conditions, in the dark and at low oxygen. The extreme traits of NMR, together with the reported genome and transcriptome information, offer unprecedented opportunities for understanding aging and advancing many other areas of biological and biomedical research.
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Affiliation(s)
- Eun Bae Kim
- Department of Bioinspired Science, Ewha Womans University, Seoul, 120-750, Korea
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Lee NK, Kim MK, Choi JH, Kim EB, Lee HG, Kang SK, Choi YJ. Identification of a peptide sequence targeting mammary vasculature via RPLP0 during lactation. Peptides 2010; 31:2247-54. [PMID: 20863866 DOI: 10.1016/j.peptides.2010.09.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 09/13/2010] [Accepted: 09/13/2010] [Indexed: 11/20/2022]
Abstract
To find novel targeting moieties to lactating mammary gland, in vivo phage display screening was conducted with lactating rats and a peptide ligand, CLHQHNQMC (designated as MG1), which specifically homes to the mammary tissue during lactation, was identified through the consecutive in vivo biopannings. MG1 peptide ligand showed specific binding affinity to lactating mammary tissue without any preference to other organs tested in ex vivo and in vivo validation, and microscopy analysis revealed that systemically introduced MG1 could be specifically localized in the lactating mammary gland associated with mammary epithelia and alveolar vasculature. Based on the observation that binding of MG1-encoding phage to lactating mammary gland was competitively inhibited by synthetic MG1 peptide ligand, we attempted to identify a counterpart molecule corresponding to specific recognition of the MG1 and the acidic Ribosomal Protein Large P0 (RPLP0) was selected as a candidate receptor for MG1 by peptide affinity pull-down assay with protein extracts from lactating mammary tissue. We demonstrated specific expression of RPLP0 in mammary tissue, especially during lactation, by immunoblotting assays and also demonstrated that MG1 peptide ligand could be bound to, and internalized into, the cells effectively via specific interaction with RPLP0 by analysis using an in vitro endothelial cell model. The overall results suggest that the MG1 has a specific affinity with RPLP0 which are dominantly expressed on the mammary vasculature during lactation and this specific affinity enables the MG1 would be served as an effective homing ligand to deliver functional molecules to the lactating mammary gland.
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Affiliation(s)
- Nam Kyung Lee
- Laboratory of Animal Cell Biotechnology, Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
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