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Song HS, Kim YB, Kim JY, Roh SW, Whon TW. Advances in Culturomics Research on the Human Gut Microbiome: Optimizing Medium Composition and Culture Techniques for Enhanced Microbial Discovery. J Microbiol Biotechnol 2024; 34:757-764. [PMID: 38379289 DOI: 10.4014/jmb.2311.11024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/29/2024] [Accepted: 02/03/2024] [Indexed: 02/22/2024]
Abstract
Despite considerable advancements achieved using next-generation sequencing technologies in exploring microbial diversity, several species of the gut microbiome remain unknown. In this transformative era, culturomics has risen to prominence as a pivotal approach in unveiling realms of microbial diversity that were previously deemed inaccessible. Utilizing innovative strategies to optimize growth and culture medium composition, scientists have successfully cultured hard-to-cultivate microbes. This progress has fostered the discovery and understanding of elusive microbial entities, highlighting their essential role in human health and disease paradigms. In this review, we emphasize the importance of culturomics research on the gut microbiome and provide new theories and insights for expanding microbial diversity via the optimization of cultivation conditions.
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Affiliation(s)
- Hye Seon Song
- Division of Environmental Materials, Honam National Institute of Biological Resource (HNIBR), Mokpo 58762, Republic of Korea
| | - Yeon Bee Kim
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju 61755, Republic of Korea
| | - Joon Yong Kim
- Microbiome Research Institute, LISCure Biosciences Inc., Gyeonggi-do 13486, Republic of Korea
| | - Seong Woon Roh
- Microbiome Research Institute, LISCure Biosciences Inc., Gyeonggi-do 13486, Republic of Korea
| | - Tae Woong Whon
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju 61755, Republic of Korea
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Mahmud MR, Jian C, Uddin MK, Huhtinen M, Salonen A, Peltoniemi O, Venhoranta H, Oliviero C. Impact of Intestinal Microbiota on Growth Performance of Suckling and Weaned Piglets. Microbiol Spectr 2023; 11:e0374422. [PMID: 37022154 PMCID: PMC10269657 DOI: 10.1128/spectrum.03744-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/13/2022] [Indexed: 04/07/2023] Open
Abstract
Small-scale studies investigating the relationship between pigs' intestinal microbiota and growth performance have generated inconsistent results. We hypothesized that on farms under favorable environmental conditions (e.g., promoting sow nest-building behavior, high colostrum production, low incidence of diseases and minimal use of antimicrobials), the piglet gut microbiota may develop toward a population that promotes growth and reduces pathogenic bacteria. Using 16S rRNA gene amplicon sequencing, we sampled and profiled the fecal microbiota from 170 individual piglets throughout suckling and postweaning periods (in total 670 samples) to track gut microbiota development and its potential association with growth. During the suckling period, the dominant genera were Lactobacillus and Bacteroides, the latter being gradually replaced by Clostridium sensu scricto 1 as piglets aged. The gut microbiota during the nursery stage, not the suckling period, predicted the average daily growth (ADG) of piglets. The relative abundances of SCFA-producing genera, in particular Faecalibacterium, Megasphaera, Mitsuokella, and Subdoligranulum, significantly correlated with high ADG of weaned piglets. In addition, the succession of the gut microbiota in high-ADG piglets occurred faster and stabilized sooner upon weaning, whereas the gut microbiota of low-ADG piglets continued to mature after weaning. Overall, our findings suggest that weaning is the major driver of gut microbiota variation in piglets with different levels of overall growth performance. This calls for further research to verify if promotion of specific gut microbiota, identified here at weaning transition, is beneficial for piglet growth. IMPORTANCE The relationship between pigs' intestinal microbiota and growth performance is of great importance for improving piglets' health and reducing antimicrobial use. We found that gut microbiota variation is significantly associated with growth during weaning and the early nursery period. Importantly, transitions toward a mature gut microbiota enriched with fiber-degrading bacteria mostly complete upon weaning in piglets with better growth. Postponing the weaning age may therefore favor the development of fiber degrading gut bacteria, conferring the necessary capacity to digest and harvest solid postweaning feed. The bacterial taxa associated with piglet growth identified herein hold potential to improve piglet growth and health.
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Affiliation(s)
- Md Rayhan Mahmud
- Department of Production Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Ching Jian
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Md Karim Uddin
- Department of Production Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | | | - Anne Salonen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Olli Peltoniemi
- Department of Production Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Heli Venhoranta
- Department of Production Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Claudio Oliviero
- Department of Production Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
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Ito K, Miyamoto H, Matsuura M, Ishii C, Tsuboi A, Tsuji N, Nakaguma T, Nakanishi Y, Kato T, Suda W, Honda F, Ito T, Moriya S, Shima H, Michibata R, Yamada R, Takahashi Y, Koga H, Kodama H, Watanabe Y, Kikuchi J, Ohno H. Noninvasive fecal metabolic profiling for the evaluation of characteristics of thermostable lactic acid bacteria, Weizmannia coagulans SANK70258, for broiler chickens. J Biosci Bioeng 2022; 134:105-115. [PMID: 35718655 DOI: 10.1016/j.jbiosc.2022.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 04/13/2022] [Accepted: 05/20/2022] [Indexed: 12/01/2022]
Abstract
Weizmannia coagulans SANK70258 is a spore-forming thermostable lactic acid bacterium and an effective probiotic for the growth of livestock animals, but its growth-promoting mechanism remains unclear. Here, the composition of fecal metabolites in broilers continuously administered with W. coagulans SANK70258 was assessed under a regular program with antibiotics, which was transiently given for 6 days after birth. Oral administration of W. coagulans to broiler chicks tended to increase the average daily gain of body weights thereafter. The composition of fecal metabolites in the early chick stage (Day 10 after birth) was dramatically altered by the continuous exposure. The levels of short-chain fatty acids (SCFAs) propionate and butyrate markedly increased, while those of acetate, one of the SCFAs, and lactate were reduced. Simultaneously, arabitol, fructose, mannitol, and erythritol, which are carbohydrates as substrates for gut microbes to produce SCFAs, also increased along with altered correlation. Correlation network analyses classified the modularity clusters (|r| > 0.7) among carbohydrates, SCFAs, lactate, amino acids, and the other metabolites under the two conditions. The characteristic diversities by the exposure were visualized beyond the perspective associated with differences in metabolite concentrations. Further, enrichment pathway analyses showed that metabolic composition related to biosynthesis and/or metabolism for SCFAs, amino acids, and energy were activated. Thus, these observations suggest that W. coagulans SANK70258 dramatically modulates the gut metabolism of the broiler chicks, and the metabolomics profiles during the early chick stages may be associated with growth promotion.
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Affiliation(s)
- Kayo Ito
- Chiba Prefectural Livestock Research Center, Yachimata, Chiba 289-1113, Japan
| | - Hirokuni Miyamoto
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8501, Japan; Sermas Co., Ltd., Chiba 263-8522, Japan; Japan Eco-science (Nikkan Kagaku) Co. Ltd., Chiba 263-8522, Japan; RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
| | - Makiko Matsuura
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8501, Japan; Sermas Co., Ltd., Chiba 263-8522, Japan
| | - Chitose Ishii
- Sermas Co., Ltd., Chiba 263-8522, Japan; RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Arisa Tsuboi
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8501, Japan; Sermas Co., Ltd., Chiba 263-8522, Japan; Japan Eco-science (Nikkan Kagaku) Co. Ltd., Chiba 263-8522, Japan; RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | | | - Teruno Nakaguma
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8501, Japan; Sermas Co., Ltd., Chiba 263-8522, Japan; Japan Eco-science (Nikkan Kagaku) Co. Ltd., Chiba 263-8522, Japan
| | - Yumiko Nakanishi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Tamotsu Kato
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Wataru Suda
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Fuyuko Honda
- Chiba Prefectural Livestock Research Center, Yachimata, Chiba 289-1113, Japan
| | - Toshiyuki Ito
- Keiyo Gas Energy Solution Co. Ltd., Ichikawa, Chiba 272-0015, Japan
| | - Shigeharu Moriya
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Hideaki Shima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | | | - Ryouichi Yamada
- Mitsubishi Chemical Corp., Marunouchi, Tokyo 100-8251, Japan
| | | | - Hirohisa Koga
- Mitsubishi Chemical Corp., Marunouchi, Tokyo 100-8251, Japan
| | - Hiroaki Kodama
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8501, Japan; Sermas Co., Ltd., Chiba 263-8522, Japan
| | - Yuko Watanabe
- Mitsubishi Chemical Corp., Marunouchi, Tokyo 100-8251, Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroshi Ohno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
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Fan Y, Xia G, Jin Y, Wang H. Ambient pH regulates lactate catabolism pathway of the ruminal Megasphaera elsdenii BE2-2083 and Selenomonas ruminantium HD4. J Appl Microbiol 2022; 132:2661-2672. [PMID: 35104035 DOI: 10.1111/jam.15464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 01/14/2022] [Accepted: 01/26/2022] [Indexed: 11/30/2022]
Abstract
AIMS To explore the impact of ambient pH on lactate catabolism by Megasphaera elsdenii BE2-2083 and Selenomonas ruminantium HD4 in both pure culture and in binary mixed culture. METHODS AND RESULTS The growth rate, substrate consumption, product formation, enzymatic activity and gene expression of M. elsdenii and S. ruminantium at various pHs were examined. Furthermore, the metabolism of lactate catabolism pathways for M. elsdenii and S. ruminantium in the co-culture system were investigated by chasing the conversion of sodium L-[3-13 C]-lactate in nuclear magnetic resonance. In the pure culture systems, ambient pH had significant effects on the growth of M. elsdenii, whereas S. ruminantium was less sensitive to pH changes. In addition, lactate metabolic genes and activities of key enzymes were affected by ambient pH in M. elsdenii and S. ruminantium. In the co-culture system, low ambient pH reduced the contribution lactate catabolism by M. elsdenii. CONCLUSION M. elsdenii BE2-2083 and S. ruminantium HD4 lactate degradation affected by ambient pH. SIGNIFICANCE AND IMPACT OF THE STUDY This study demonstrates the regulatory mechanisms of lactate decomposing bacteria in lactate catabolism under the condition of subacute ruminal acidosis.
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Affiliation(s)
- Yaotian Fan
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Guangliang Xia
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yaqian Jin
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Hongrong Wang
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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Duarte ME, Kim SW. Intestinal microbiota and its interaction to intestinal health in nursery pigs. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2022; 8:169-184. [PMID: 34977387 PMCID: PMC8683651 DOI: 10.1016/j.aninu.2021.05.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/20/2021] [Accepted: 05/07/2021] [Indexed: 02/07/2023]
Abstract
The intestinal microbiota has gained increased attention from researchers within the swine industry due to its role in promoting intestinal maturation, immune system modulation, and consequently the enhancement of the health and growth performance of the host. This review aimed to provide updated scientific information on the interaction among intestinal microbiota, dietary components, and intestinal health of pigs. The small intestine is a key site to evaluate the interaction of the microbiota, diet, and host because it is the main site for digestion and absorption of nutrients and plays an important role within the immune system. The diet and its associated components such as feed additives are the main factors affecting the microbial composition and is central in stimulating a beneficial population of microbiota. The microbiota–host interaction modulates the immune system, and, concurrently, the immune system helps to modulate the microbiota composition. The direct interaction between the microbiota and the host is an indication that the mucosa-associated microbiota can be more effective in evaluating its effect on health parameters. It was demonstrated that the mucosa-associated microbiota should be evaluated when analyzing the interaction among diets, microbiota, and health. In addition, supplementation of feed additives aimed to promote the intestinal health of pigs should consider their roles in the modulation of mucosa-associated microbiota as biomarkers to predict the response of growth performance to dietary interventions.
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Affiliation(s)
- Marcos Elias Duarte
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27695, United States
| | - Sung Woo Kim
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27695, United States
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Zhe L, Yang L, Lin S, Chen F, Wang P, Heres L, Zhuo Y, Tang J, Lin Y, Xu S, Zhang X, Jiang X, Huang L, Zhang R, Che L, Tian G, Feng B, Wu D, Fang Z. Differential responses of weaned piglets to supplemental porcine or chicken plasma in diets without inclusion of antibiotics and zinc oxide. ACTA ACUST UNITED AC 2021; 7:1173-1181. [PMID: 34754959 PMCID: PMC8556524 DOI: 10.1016/j.aninu.2021.05.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/04/2021] [Accepted: 05/20/2021] [Indexed: 12/01/2022]
Abstract
This study was conducted to investigate the effects of spray-dried porcine plasma protein (SDPP) or spray-dried chicken plasma protein (SDCP) supplementation in diets without the inclusion of antibiotics and zinc oxide (ZnO) on growth performance, fecal score, and fecal microbiota in early-weaned piglets. A total of 192 healthy weaning piglets (Duroc × Landrace × Yorkshire, 21 d old) were blocked by BW (6.53 ± 0.60 kg) and randomly assigned to 4 dietary treatments: negative control (NC, basal diet), positive control (PC), basal diet + ZnO at 2 g/kg and antibiotics at 0.8 g/kg), SDPP (containing 5% SDPP), and SDCP (containing 5% SDCP). The experiment lasted 14 d. The SDPP group had higher (P < 0.05) final BW, average daily gain and average daily feed intake than the NC and SDCP groups. The percentage of piglets with fecal scores at 2 or ≥2 was higher (P < 0.05) in the NC and SDCP groups than in the PC group. A decreased (P < 0.05) bacterial alpha diversity and Bacteroidetes abundance, but increased (P < 0.05) Firmicutes abundance were observed in the PC and SDPP groups when compared to the NC group. The relative abundance of Lactobacillus was higher (P < 0.05) in the SDPP than in the SDCP group, and that of Streptococcus was higher (P < 0.01) in the PC and SDPP groups than in the NC group. The PC group also had higher (P < 0.01) Faecalibacterium abundance than the NC and SDCP groups. Additionally, the SDCP group had higher (P < 0.05) serum urea nitrogen than those fed other diets, and lower (P < 0.10) short-chain fatty acids to branched-chain fatty acids ratio than the PC and SDPP groups. Overall, SDPP was a promising animal protein for piglets in increasing feed intake, modifying gut microbiota profile, reducing gut protein fermentation and alleviating diarrhea frequency, thus promoting growth performance, under the conditions with limited in-feed utilization of antibiotics and ZnO.
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Affiliation(s)
- Li Zhe
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Lunxiang Yang
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Sen Lin
- Sericultural & Agri-Food Research Institute Guangdong Academy of Agricultural Sciences, 133 Dongguanzhuang Yiheng Road, Guangzhou, 510610, China
| | - Fangyuan Chen
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Peng Wang
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Lourens Heres
- Sonac (China) Biology Co., Ltd, Shanghai, 1668 Xiuyan Road, Pudong New Area, Shanghai, 200120, China
| | - Yong Zhuo
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Jiayong Tang
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Yan Lin
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Shengyu Xu
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Xiaoling Zhang
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Xuemei Jiang
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Lingjie Huang
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Ruinan Zhang
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Lianqiang Che
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Gang Tian
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Bin Feng
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - De Wu
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Zhengfeng Fang
- Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
- Corresponding author.
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Gu Y, Yan D, Wu M, Li M, Li P, Wang J, Chang Y, Yang F, Di S, Ni S, Yang M, Liu J. Influence of the densities and nutritional components of bacterial colonies on the culture-enriched gut bacterial community structure. AMB Express 2021; 11:78. [PMID: 34057622 PMCID: PMC8167003 DOI: 10.1186/s13568-021-01240-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 05/24/2021] [Indexed: 11/10/2022] Open
Abstract
Isolating relevant microorganisms is still a substantial challenge that limits the use of bacteria in the maintenance of human health. To confirm which media and which bacterial colony densities can enrich certain kinds of bacteria, we selected eight common media and used them to enrich the gut microorganisms on agar plates. Then, we calculated the numbers of bacterial colonies and collected the bacterial culture mixtures from each kind of medium. Using the Illumina HiSeq platform, we analyzed the composition and diversity of the culture-enriched gut bacterial community. Our data suggested that medium supplemented with blood could increase the diversity of the bacterial community. In addition, beef powder and peptone could significantly change the culture-enriched bacterial community. A moderate density (100-150 colony-forming units per plate) was optimal for obtaining the highest diversity on the agar. Similarly, membrane transport was significantly enriched in the moderate-density group, which indicated a more active metabolism in this density range. Overall, these results reveal the optimal culture conditions, including the densities of colonies and nutritional components for various gut bacteria, that provide a novel strategy for isolating bacteria in a way that is targeted and avoids blinded and repetitive work.
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Reddy KE, Kim M, Kim KH, Ji SY, Baek Y, Chun JL, Jung HJ, Choe C, Lee HJ, Kim M, Lee SD. Effect of commercially purified deoxynivalenol and zearalenone mycotoxins on microbial diversity of pig cecum contents. Anim Biosci 2020; 34:243-255. [PMID: 32777887 PMCID: PMC7876725 DOI: 10.5713/ajas.20.0137] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/27/2020] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVE Deoxynivalenol (DON) and zearalenone (ZEN) are mycotoxins that frequently contaminate maize and grain cereals, imposing risks to the health of both humans and animals and leading to economic losses. The gut microbiome has been shown to help combat the effects of such toxins, with certain microorganisms reported to contribute significantly to the detoxification process. METHODS We examined the cecum contents of three different dietary groups of pigs (control, as well as diets contaminated with 8 mg DON/kg feed or 0.8 mg ZEN/kg feed). Bacterial 16S rRNA gene amplicons were acquired from the cecum contents and evaluated by next-generation sequencing. RESULTS A total of 2,539,288 sequences were generated with ~500 nucleotide read lengths. Firmicutes, Bacteroidetes, and Proteobacteria were the dominant phyla, occupying more than 96% of all three groups. Lactobacillus, Bacteroides, Megasphaera, and Campylobacter showed potential as biomarkers for each group. Particularly, Lactobacillus and Bacteroides were more abundant in the DON and ZEN groups than in the control. Additionally, 52,414 operational taxonomic units were detected in the three groups; those of Bacteroides, Lactobacillus, Campylobacter, and Prevotella were most dominant and significantly varied between groups. Hence, contamination of feed by DON and ZEN affected the cecum microbiota, while Lactobacillus and Bacteroides were highly abundant and positively influenced the host physiology. CONCLUSION Lactobacillus and Bacteroides play key roles in the process of detoxification and improving the immune response. We, therefore, believe that these results may be useful for determining whether disturbances in the intestinal microflora, such as the toxic effects of DON and ZEN, can be treated by modulating the intestinal bacterial flora.
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Affiliation(s)
- Kondreddy Eswar Reddy
- Animal Nutrition and Physiology Team, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea
| | - Minji Kim
- Animal Nutrition and Physiology Team, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea
| | - Ki Hyun Kim
- Animal Nutrition and Physiology Team, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea
| | - Sang Yun Ji
- Animal Nutrition and Physiology Team, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea
| | - Youlchang Baek
- Animal Nutrition and Physiology Team, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea
| | - Ju Lan Chun
- Animal Nutrition and Physiology Team, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea
| | - Hyun Jung Jung
- Animal Nutrition and Physiology Team, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea.,Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan 31000, Korea
| | - Changyong Choe
- Division of Animal Disease and Health, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea
| | - Hyun Jeong Lee
- Animal Nutrition and Physiology Team, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea.,Dairy Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan 31000, Korea
| | - Minseok Kim
- Animal Nutrition and Physiology Team, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea.,Department of Animal Science, College of Agriculture and Life Science, Chonnam National University, Gwangju 61186, Korea
| | - Sung Dae Lee
- Animal Nutrition and Physiology Team, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea
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Yoshikawa S, Araoka R, Kajihara Y, Ito T, Miyamoto H, Kodama H. Valerate production by Megasphaera elsdenii isolated from pig feces. J Biosci Bioeng 2018; 125:519-524. [DOI: 10.1016/j.jbiosc.2017.12.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 11/29/2017] [Accepted: 12/19/2017] [Indexed: 02/06/2023]
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10
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Dong B, Liu S, Wang C, Cao Y. Effects of xylanase supplementation to wheat-based diets on growth performance, nutrient digestibility and gut microbes in weanling pigs. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2018. [PMID: 29531194 PMCID: PMC6127568 DOI: 10.5713/ajas.17.0867] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE This study was designed to investigate the effects of an Aspergillus sulphureus xylanase expressed in Pichia pastoris on the growth performance, nutrient digestibility and gut microbes in weanling pigs. METHODS A total of 180 weanling pigs (initial body weights were 8.47±1.40 kg) were assigned randomly to 5 dietary treatments. Each treatment had 6 replicates with 6 pigs per replicate. The experimental diets were wheat based with supplementation of 0, 500, 1,000, 2,000, and 4,000 U xylanase/kg. The experiment lasted 28 days (early phase, d 0 to 14; late phase, d 15 to 28). RESULTS In the early phase, compared to the control, average daily gain (ADG) was higher for pigs fed diets supplemented with xylanase and there was a quadratic response in ADG (p<0.05). In the entire phase, ADG was higher for the pigs fed 1,000 or 2,000 U/kg xylanase compared to the control (p<0.05). The gain to feed ratio was higher for pigs fed diets supplemented with 1,000 or 2,000 U/kg xylanase compared to the control (p<0.05). Increasing the amount of xylanase improved the apparent total tract digestibility of dry matter, crude protein, neutral detergent fiber, calcium, and phosphorus during both periods (p<0.05). Xylanase supplementation (2,000 U/kg) decreased the proportion of Lachnospiraceae (by 50%) in Firmicutes, but increased Prevotellaceae (by 175%) in Bacteroidetes and almost diminished Enterobacteriaceae (Escherichia-Shigella) in Proteobacteria. CONCLUSION Xylanase supplementation increased growth performance and nutrient digestibility up to 2,000 U/kg. Supplementation of xylanase (2,000 U/kg) decreased the richness of gut bacteria but diminished the growth of harmful pathogenic bacteria, such as Escherichia-Shigella, in the colon.
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Affiliation(s)
- Bing Dong
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing 100193, China.,Beijing Key Laboratory of Biofeed Additives, China Agricultural University, Beijing 100193, China
| | - Shaoshuai Liu
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing 100193, China.,Beijing Key Laboratory of Biofeed Additives, China Agricultural University, Beijing 100193, China
| | - Chunlin Wang
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing 100193, China.,Beijing Key Laboratory of Biofeed Additives, China Agricultural University, Beijing 100193, China
| | - Yunhe Cao
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing 100193, China.,Beijing Key Laboratory of Biofeed Additives, China Agricultural University, Beijing 100193, China
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