1
|
Zhang C, Jiang X, Wu S, Zhang J, Wang Y, Li Z, Yao J. Dietary fat and carbohydrate-balancing the lactation performance and methane emissions in the dairy cow industry: A meta-analysis. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2024; 17:347-357. [PMID: 38800741 PMCID: PMC11127094 DOI: 10.1016/j.aninu.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 01/11/2024] [Accepted: 02/20/2024] [Indexed: 05/29/2024]
Abstract
For the agroecosystems of the dairy cow industry, dietary carbohydrate (starch, neutral detergent fiber [NDF]) and fat could directly affect rumen methane emissions and host energy utilization. However, the relationships among diet, lactation performance, and methane emissions need to be further determined to assist dairy farms to adjust diet formulations and feeding strategies for environmental and production management. A meta-analysis was conducted in the current study to explore quantitative patterns of dietary fat and carbohydrate at different levels in balancing lactation performance and environment sustainability of dairy cows, and to establish a methane emission prediction model using the artificial neural network (ANN) model. The results showed that the regression relationship between dietary fat, carbohydrate and methane emissions could be shown by the following models: methane = 106.78 + (14.86 × DMI), R2 = 0.80; methane = 443.17 - (46.41 × starch/NDF), R2 = 0.76; and methane = 388.91 + (31.40 × fat) - (5.42 × fat2), R2 = 0.80. The regression relationships between dietary fat, carbohydrate and lactation performance could be shown by the following models: milk fat yield = 1.08 + (0.43 × starch/NDF) - [0.34 × (starch/NDF)2], R2 = 0.79; milk protein yield = 0.68 + (0.15 × fat) - (0.016 × fat2), R2 = 0.82. In the structural equation model, we found that when formulating dietary carbohydrates and fats, it was necessary to balance the relationship between methane emissions and lactation performance. Specifically, dietary starch/NDF was lower than 0.63 (extremum point) and dietary fat was between 2.89% and 4.69% (extremum point), it could ensure that the aim of methane emission reduction (methane emissions decrease with increasing dietary starch/NDF and fat) was achieved without losing lactation performance of dairy cows (lactation performance increase with increasing dietary starch/NDF and fat). Finally, we established the ANN model to predict methane emissions (training set: R2 = 0.62; validation set: R2 = 0.61).
Collapse
Affiliation(s)
| | | | - Shengru Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jun Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yue Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Zongjun Li
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Junhu Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| |
Collapse
|
2
|
Wu S, Chen X, Cai R, Chen X, Zhang J, Xie J, Shen M. Sulfated Chinese Yam Polysaccharides Alleviate LPS-Induced Acute Inflammation in Mice through Modulating Intestinal Microbiota. Foods 2023; 12:foods12091772. [PMID: 37174310 PMCID: PMC10178587 DOI: 10.3390/foods12091772] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 04/14/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023] Open
Abstract
This study aimed to test the preventive anti-inflammatory properties of Chinese yam polysaccharides (CYP) and sulfated Chinese yam polysaccharides (SCYP) on LPS-induced systemic acute inflammation in mice and investigate their mechanisms of action. The results showed that SCYP can efficiently reduce plasma TNF-α and IL-6 levels, exhibiting an obvious anti-inflammation ability. Moreover, SCYP reduced hepatic TNF-α, IL-6, and IL-1β secretion more effectively than CYP, and significantly altered intestinal oxidative stress levels. In addition, a 16S rRNA gene sequencing analysis showed that CYP regulated the gut microbiota by decreasing Desulfovibrio and Sutterella and increasing Prevotella. SCYP changed the gut microbiota by decreasing Desulfovibrio and increasing Coprococcus, which reversed the microbiota dysbiosis caused by LPS. Linear discriminant analysis (LDA) effect size (LEfSe) revealed that treatment with CYP and SCYP can produce more biomarkers of the gut microbiome that can promote the proliferation of polysaccharide-degrading bacteria and facilitate the intestinal de-utilization of polysaccharides. These results suggest that SCYP can differentially regulate intestinal flora, and that they exhibit anti-inflammatory effects, thus providing a new reference to rationalize the exploitation of sulfated yam polysaccharides.
Collapse
Affiliation(s)
- Shihua Wu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Xianxiang Chen
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Ruixin Cai
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Xiaodie Chen
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Jian Zhang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Jianhua Xie
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Mingyue Shen
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
| |
Collapse
|
3
|
Feehan B, Ran Q, Dorman V, Rumback K, Pogranichniy S, Ward K, Goodband R, Niederwerder MC, Summers KL, Lee STM. Stability and volatility shape the gut bacteriome and Kazachstania slooffiae dynamics in preweaning, nursery and adult pigs. Sci Rep 2022; 12:15080. [PMID: 36064754 PMCID: PMC9445069 DOI: 10.1038/s41598-022-19093-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/24/2022] [Indexed: 11/09/2022] Open
Abstract
The gut microbiome plays important roles in the maintenance of health and pathogenesis of diseases in the growing host. In order to fully comprehend the interplay of the gut microbiome and host, a foundational understanding of longitudinal microbiome, including bacteria and fungi, development is necessary. In this study, we evaluated enteric microbiome and host dynamics throughout the lifetime of commercial swine. We collected a total of 234 fecal samples from ten pigs across 31 time points in three developmental stages (5 preweaning, 15 nursery, and 11 growth adult). We then performed 16S rRNA gene amplicon sequencing for bacterial profiles and qPCR for the fungus Kazachstania slooffiae. We identified distinct bacteriome clustering according to the host developmental stage, with the preweaning stage exhibiting low bacterial diversity and high volatility amongst samples. We further identified clusters of bacteria that were considered core, increasing, decreasing or stage-associated throughout the host lifetime. Kazachstania slooffiae was absent in the preweaning stage but peaked during the nursery stage of the host. We determined that all host growth stages contained negative correlations between K. slooffiae and bacterial genera, with only the growth adult stage containing positive correlates. Our stage-associated bacteriome results suggested the neonate contained a volatile gut microbiome. Upon weaning, the microbiome became relatively established with comparatively fewer perturbations in microbiome composition. Differential analysis indicated bacteria might play distinct stage-associated roles in metabolism and pathogenesis. The lack of positive correlates and shared K. slooffiae-bacteria interactions between stages warranted future research into the interactions amongst these kingdoms for host health. This research is foundational for understanding how bacteria and fungi develop singularly, as well as within a complex ecosystem in the host's gut environment.
Collapse
Affiliation(s)
- Brandi Feehan
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Qinghong Ran
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Victoria Dorman
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Kourtney Rumback
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Sophia Pogranichniy
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Kaitlyn Ward
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Robert Goodband
- Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS, 66506, USA
| | - Megan C Niederwerder
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA.,Swine Health Information Center, Ames, IA, 50010, USA
| | - Katie Lynn Summers
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Center, United States Department of Agriculture, Beltsville, MD, 20705, USA
| | - Sonny T M Lee
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA.
| |
Collapse
|
4
|
Li QS, Wang R, Ma ZY, Zhang XM, Jiao JZ, Zhang ZG, Ungerfeld EM, Yi KL, Zhang BZ, Long L, Long Y, Tao Y, Huang T, Greening C, Tan ZL, Wang M. Dietary selection of metabolically distinct microorganisms drives hydrogen metabolism in ruminants. THE ISME JOURNAL 2022; 16:2535-2546. [PMID: 35931768 PMCID: PMC9562222 DOI: 10.1038/s41396-022-01294-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 06/29/2022] [Accepted: 07/11/2022] [Indexed: 11/09/2022]
Abstract
Ruminants are important for global food security but emit the greenhouse gas methane. Rumen microorganisms break down complex carbohydrates to produce volatile fatty acids and molecular hydrogen. This hydrogen is mainly converted into methane by archaea, but can also be used by hydrogenotrophic acetogenic and respiratory bacteria to produce useful metabolites. A better mechanistic understanding is needed on how dietary carbohydrates influence hydrogen metabolism and methanogenesis. We profiled the composition, metabolic pathways, and activities of rumen microbiota in 24 beef cattle adapted to either fiber-rich or starch-rich diets. The fiber-rich diet selected for fibrolytic bacteria and methanogens resulting in increased fiber utilization, while the starch-rich diet selected for amylolytic bacteria and lactate utilizers, allowing the maintenance of a healthy rumen and decreasing methane production (p < 0.05). Furthermore, the fiber-rich diet enriched for hydrogenotrophic methanogens and acetogens leading to increased electron-bifurcating [FeFe]-hydrogenases, methanogenic [NiFe]- and [Fe]-hydrogenases and acetyl-CoA synthase, with lower dissolved hydrogen (42%, p < 0.001). In contrast, the starch-rich diet enriched for respiratory hydrogenotrophs with greater hydrogen-producing group B [FeFe]-hydrogenases and respiratory group 1d [NiFe]-hydrogenases. Parallel in vitro experiments showed that the fiber-rich selected microbiome enhanced acetate and butyrate production while decreasing methane production (p < 0.05), suggesting that the enriched hydrogenotrophic acetogens converted some hydrogen that would otherwise be used by methanogenesis. These insights into hydrogen metabolism and methanogenesis improve understanding of energy harvesting strategies, healthy rumen maintenance, and methane mitigation in ruminants.
Collapse
Affiliation(s)
- Qiu Shuang Li
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Rong Wang
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - Zhi Yuan Ma
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiu Min Zhang
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - Jin Zhen Jiao
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - Zhi Gang Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Emilio M Ungerfeld
- Centro Regional de Investigación Carillanca, Instituto de Investigaciones Agropecuarias (INIA), Temuco, Chile
| | - Kang Le Yi
- Hunan Institute of Animal and Veterinary Science, Changsha, Hunan, China.,Xiangxi Cattle Engineering Technology Center of Hunan Province, Huayuan, Hunan, China
| | - Bai Zhong Zhang
- Hunan Institute of Animal and Veterinary Science, Changsha, Hunan, China.,Xiangxi Cattle Engineering Technology Center of Hunan Province, Huayuan, Hunan, China
| | - Liang Long
- Xiangxi Cattle Engineering Technology Center of Hunan Province, Huayuan, Hunan, China.,Hunan De Nong Animal Husbandry Group Co. Ltd, Huayuan, Hunan, China
| | - Yun Long
- Xiangxi Cattle Engineering Technology Center of Hunan Province, Huayuan, Hunan, China.,Hunan De Nong Animal Husbandry Group Co. Ltd, Huayuan, Hunan, China
| | - Ye Tao
- Shanghai BIOZERON Biotechnology Company Ltd, Shanghai, China
| | - Tao Huang
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Chris Greening
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Australia
| | - Zhi Liang Tan
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China. .,University of Chinese Academy of Sciences, Beijing, China.
| | - Min Wang
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China. .,University of Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
5
|
Li Y, Bi Y, Yang L, Jin K. Comparative study on intestinal microbiome composition and function in young and adult Hainan gibbons ( Nomascus hainanus). PeerJ 2022; 10:e13527. [PMID: 35698614 PMCID: PMC9188309 DOI: 10.7717/peerj.13527] [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: 03/15/2022] [Accepted: 05/11/2022] [Indexed: 01/17/2023] Open
Abstract
The Hainan gibbon is one of the most endangered primates in the world, with a small population size, narrow distribution range, and high inbreeding risk, which retains the risk of species extinction. To explore the composition and functional differences of the intestinal microbiome of Hainan gibbons at different ages, the faecal microbiomes of young and adult Hainan gibbons were analysed using metagenome sequencing. The results showed that the dominant phyla in the intestinal tract of young and adult Hainan gibbons were Firmicutes and Bacteroidetes, and the dominant genus was Prevotella. Linear discriminant analysis effect size analysis showed that Firmicutes, Ruminococcus, Clostridium, and Butyrivibrio were significantly more abundant in adults than in young, whereas Bacteroidetes, Proteobacteria, Prevotella, and Bacteroides were significantly more abundant in young than in adults. In terms of gene function, the adult Hainan gibbon intestinal microbiome generally harboured a higher abundance of genes related to metabolic processes, such as carbohydrate, amino acid, and nucleotide metabolism. This may be due to adaptive advantages for adult Hainan gibbons, such as stable and mature intestinal microbiome composition, which allows them to utilise diverse foods efficiently. In summary, this study helps understand the dynamic changes in the intestinal microbiome of young and adult Hainan gibbons and plays a key role in the health monitoring and rejuvenation of their population.
Collapse
Affiliation(s)
- Yimeng Li
- Institute of Forest Ecology-Environment and Nature Conservation, Chinese Academy of Forestry, Beijing, China,Beijing Museum of Natural History, Beijing, China,Hainan Institute of National Park, Haikou, China
| | - Yu Bi
- Institute of Forest Ecology-Environment and Nature Conservation, Chinese Academy of Forestry, Beijing, China,Hainan Institute of National Park, Haikou, China,Research Institute of Natural Protected Area, Chinese Academy of Forestry, Beijing, China,Key Laboratory of Biodiversity Conservation of National Forestry and Grassland Administration, Beijing, China
| | - Liangliang Yang
- Institute of Forest Ecology-Environment and Nature Conservation, Chinese Academy of Forestry, Beijing, China,Key Laboratory of Biodiversity Conservation of National Forestry and Grassland Administration, Beijing, China
| | - Kun Jin
- Institute of Forest Ecology-Environment and Nature Conservation, Chinese Academy of Forestry, Beijing, China,Hainan Institute of National Park, Haikou, China,Research Institute of Natural Protected Area, Chinese Academy of Forestry, Beijing, China,Key Laboratory of Biodiversity Conservation of National Forestry and Grassland Administration, Beijing, China
| |
Collapse
|
6
|
Wang Y, Tian L, Sun L, Zhou W, Zhi W, Qing J, Abdi Saed Y, Dong L, Zhang X, Li Y. Gut Microbes in Immunoglobulin A Nephropathy and Their Potential Therapeutic Applications. Front Med (Lausanne) 2022; 9:823267. [PMID: 35655857 PMCID: PMC9152025 DOI: 10.3389/fmed.2022.823267] [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: 11/27/2021] [Accepted: 04/15/2022] [Indexed: 11/13/2022] Open
Abstract
Microbial ecosystem consists of a complex community of bacterial interactions and its host microenvironment (tissue, cell, metabolite). Because the interaction between gut microbiota and host involves many diseases and seriously affects human health, the study of the interaction mechanism between gut microbiota and host has attracted great attention. The gut microbiome is made up of 100 trillion bacteria that have both beneficial and adverse effects on human health. The development of IgA Nephropathy results in changes in the intestinal microbial ecosystem that affect host physiology and health. Similarly, changes in intestinal microbiota also affect the development of IgA Nephropathy. Thus, the gut microbiome represents a novel therapeutic target for improving the outcome of IgA Nephropathy, including hematuria symptoms and disease progression. In this review, we summarize the effect of intestinal microbiota on IgA Nephropathy in recent years and it has been clarified that the intestinal microbiota has a great influence on the pathogenesis and treatment of IgA Nephropathy.
Collapse
Affiliation(s)
- Yi Wang
- The Third Clinical College, Shanxi University of Chinese Medicine, Taiyuan, China
| | - Lingling Tian
- The Third Clinical College, Shanxi University of Chinese Medicine, Taiyuan, China
| | - Lin Sun
- College of Traditional Chinese Medicine and Food Engineering, Shanxi University of Chinese Medicine, Jinzhong, China
| | - Wenjing Zhou
- School of Medical Sciences, Shanxi University of Chinese Medicine, Jinzhong, China
| | - Wenqiang Zhi
- The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, China
| | - Jianbo Qing
- The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, China
| | - Yasin Abdi Saed
- Department of Nephrology, Shanxi Provincial People's Hospital (Fifth Hospital) of Shanxi Medical University, Taiyuan, China
| | - Lina Dong
- Core Laboratory, Shanxi Provincial People's Hospital (Fifth Hospital) of Shanxi Medical University, Taiyuan, China
| | - Xiadong Zhang
- Core Laboratory, Shanxi Provincial People's Hospital (Fifth Hospital) of Shanxi Medical University, Taiyuan, China
| | - Yafeng Li
- Department of Nephrology, Shanxi Provincial People's Hospital (Fifth Hospital) of Shanxi Medical University, Taiyuan, China.,Core Laboratory, Shanxi Provincial People's Hospital (Fifth Hospital) of Shanxi Medical University, Taiyuan, China.,Shanxi Provincial Key Laboratory of Kidney Disease, Taiyuan, China.,Academy of Microbial Ecology, Shanxi Medical University, Taiyuan, China
| |
Collapse
|
7
|
Huang J, Lin B, Zhang Y, Xie Z, Zheng Y, Wang Q, Xiao H. Bamboo shavings derived O-acetylated xylan alleviates loperamide-induced constipation in mice. Carbohydr Polym 2022; 276:118761. [PMID: 34823784 DOI: 10.1016/j.carbpol.2021.118761] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 09/15/2021] [Accepted: 10/10/2021] [Indexed: 12/22/2022]
Abstract
BSH-1 is an O-acetylated xylan obtained from bamboo shavings. This study determined the protective effects of BSH-1 against loperamide (Lop)-induced constipation in mice. Mice received BSH-1 by gavage daily for 14 days. In constipated mice, BSH-1 significantly shortened the defecation time and raised the gastrointestinal (GI) transit rate, stool production, and cecal concentration of short-chain fatty acids (SCFAs). BSH-1 regulated the serum levels of gut hormones and neurotransmitters. BSH-1 also significantly altered the cecal microbiota of the constipated mice by increasing the abundance of potentially beneficial bacteria (e.g., Lactobacillus, Roseburia, and Bacteroidales_S24-7) and decreasing potentially pathogenic bacteria (e.g., Alloprevotella and Staphylococcus). Furthermore, colonic transcriptome analysis revealed that BSH-1 significantly reversed the expression changes of genes related to intestinal motility, water and ion transport, inflammation and cancer in constipated mice. Our findings indicated that BSH-1 effectively relieved Lop-induced constipation in mice and could be potentially used for constipation treatment.
Collapse
Affiliation(s)
- Juqing Huang
- Institute of Agricultural Engineering, Fujian Academy of Agricultural Sciences, Fuzhou 350003, PR China; Department of Food Science, University of Massachusetts Amherst, Amherst, USA
| | - Bin Lin
- Institute of Agricultural Engineering, Fujian Academy of Agricultural Sciences, Fuzhou 350003, PR China
| | - Ying Zhang
- Department of Food Science and Nutrition, School of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, PR China
| | - Zhenglu Xie
- Jinshan College of Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Yi Zheng
- Institute of Agricultural Engineering, Fujian Academy of Agricultural Sciences, Fuzhou 350003, PR China
| | - Qi Wang
- Department of Food Science, University of Massachusetts Amherst, Amherst, USA
| | - Hang Xiao
- Department of Food Science, University of Massachusetts Amherst, Amherst, USA.
| |
Collapse
|
8
|
Dohnálek J, Dušková J, Tishchenko G, Kolenko P, Skálová T, Novák P, Fejfarová K, Šimůnek J. Chitinase Chit62J4 Essential for Chitin Processing by Human Microbiome Bacterium Clostridium paraputrificum J4. Molecules 2021; 26:molecules26195978. [PMID: 34641521 PMCID: PMC8512545 DOI: 10.3390/molecules26195978] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 12/26/2022] Open
Abstract
Commensal bacterium Clostridium paraputrificum J4 produces several extracellular chitinolytic enzymes including a 62 kDa chitinase Chit62J4 active toward 4-nitrophenyl N,N'-diacetyl-β-d-chitobioside (pNGG). We characterized the crude enzyme from bacterial culture fluid, recombinant enzyme rChit62J4, and its catalytic domain rChit62J4cat. This major chitinase, securing nutrition of the bacterium in the human intestinal tract when supplied with chitin, has a pH optimum of 5.5 and processes pNGG with Km = 0.24 mM and kcat = 30.0 s-1. Sequence comparison of the amino acid sequence of Chit62J4, determined during bacterial genome sequencing, characterizes the enzyme as a family 18 glycosyl hydrolase with a four-domain structure. The catalytic domain has the typical TIM barrel structure and the accessory domains-2x Fn3/Big3 and a carbohydrate binding module-that likely supports enzyme activity on chitin fibers. The catalytic domain is highly homologous to a single-domain chitinase of Bacillus cereus NCTU2. However, the catalytic profiles significantly differ between the two enzymes despite almost identical catalytic sites. The shift of pI and pH optimum of the commensal enzyme toward acidic values compared to the soil bacterium is the likely environmental adaptation that provides C. paraputrificum J4 a competitive advantage over other commensal bacteria.
Collapse
Affiliation(s)
- Jan Dohnálek
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, v. v. i., Biocev, Průmyslová 595, 252 50 Vestec, Czech Republic; (J.D.); (P.K.); (T.S.); (K.F.)
- Correspondence: ; Tel.: +420-325-873-758; Fax: +420-325-873-710
| | - Jarmila Dušková
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, v. v. i., Biocev, Průmyslová 595, 252 50 Vestec, Czech Republic; (J.D.); (P.K.); (T.S.); (K.F.)
| | - Galina Tishchenko
- Department of Structural Analysis of Biomacromolecules, Institute of Macromolecular Chemistry of the Czech Academy of Sciences, v. v. i., Heyrovsky Sq. 2, 162 06 Prague, Czech Republic;
| | - Petr Kolenko
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, v. v. i., Biocev, Průmyslová 595, 252 50 Vestec, Czech Republic; (J.D.); (P.K.); (T.S.); (K.F.)
| | - Tereza Skálová
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, v. v. i., Biocev, Průmyslová 595, 252 50 Vestec, Czech Republic; (J.D.); (P.K.); (T.S.); (K.F.)
| | - Petr Novák
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, v. v. i., Biocev, Průmyslová 595, 252 50 Vestec, Czech Republic;
| | - Karla Fejfarová
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, v. v. i., Biocev, Průmyslová 595, 252 50 Vestec, Czech Republic; (J.D.); (P.K.); (T.S.); (K.F.)
| | - Jiří Šimůnek
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, v. v. i., Vídeňská 1083, 142 00 Prague, Czech Republic;
| |
Collapse
|
9
|
Harriman R, Lewis JS. Bioderived materials that disarm the gut mucosal immune system: Potential lessons from commensal microbiota. Acta Biomater 2021; 133:187-207. [PMID: 34098091 DOI: 10.1016/j.actbio.2021.05.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/25/2021] [Accepted: 05/20/2021] [Indexed: 12/12/2022]
Abstract
Over the course of evolution, mammals and gut commensal microbes have adapted to coexist with each other. This homeostatic coexistence is dependent on an intricate balance between tolerogenic and inflammatory responses directed towards beneficial, commensal microbes and pathogenic intruders, respectively. Immune tolerance towards the gut microflora is largely sustained by immunomodulatory molecules produced by the commensals, which protect the bacteria from immune advances and maintain the gut's unique tolerogenic microenvironment, as well as systemic homeostasis. The identification and characterization of commensal-derived, tolerogenic molecules could lead to their utilization in biomaterials-inspired delivery schemes involving nano/microparticles or hydrogels, and potentially lead to the next generation of commensal-derived therapeutics. Moreover, gut-on-chip technologies could augment the discovery and characterization of influential commensals by providing realistic in vitro models conducive to finicky microbes. In this review, we provide an overview of the gut immune system, describe its intricate relationships with the microflora and identify major genera involved in maintaining tolerogenic responses and peripheral homeostasis. More relevant to biomaterials, we discuss commensal-derived molecules that are known to interface with immune cells and discuss potential strategies for their incorporation into biomaterial-based strategies aimed at culling inflammatory diseases. We hope this review will bridge the current findings in gut immunology, microbiology and biomaterials and spark further investigation into this emerging field. STATEMENT OF SIGNIFICANCE: Despite its tremendous potential to culminate into revolutionary therapeutics, the synergy between immunology, microbiology, and biomaterials has only been explored at a superficial level. Strategic incorporation of biomaterial-based technologies may be necessary to fully characterize and capitalize on the rapidly growing repertoire of immunomodulatory molecules derived from commensal microbes. Bioengineers may be able to combine state-of-the-art delivery platforms with immunomodulatory cues from commensals to provide a more holistic approach to combating inflammatory disease. This interdisciplinary approach could potentiate a neoteric field of research - "commensal-inspired" therapeutics with the promise of revolutionizing the treatment of inflammatory disease.
Collapse
Affiliation(s)
- Rian Harriman
- University of California Davis, Department of Biomedical Engineering, Davis, CA 95616, USA
| | - Jamal S Lewis
- University of California Davis, Department of Biomedical Engineering, Davis, CA 95616, USA.
| |
Collapse
|
10
|
An J, Lee H, Lee S, Song Y, Kim J, Park IH, Kong H, Kim K. Modulation of Pro-inflammatory and Anti-inflammatory Cytokines in the Fat by an Aloe Gel-based Formula, QDMC, Is Correlated with Altered Gut Microbiota. Immune Netw 2021; 21:e15. [PMID: 33996171 PMCID: PMC8099612 DOI: 10.4110/in.2021.21.e15] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 01/08/2023] Open
Abstract
Abnormal inflammatory responses are closely associated with intestinal microbial dysbiosis. Oral administration of Qmatrix-diabetes-mellitus complex (QDMC), an Aloe gel-based formula, has been reported to improve inflammation in type 2 diabetic mice; however, the role of the gut microbiota in ameliorating efficacy of QDMC remains unclear. We investigated the effect of QDMC on the gut microbiota in a type 2 diabetic aged mouse model that was administered a high-fat diet. Proinflammatory (TNF-α and IL-6) and anti-inflammatory (IL-4 and IL-10) cytokine levels in the fat were normalized via oral administration of QDMC, and relative abundances of Bacteroides, Butyricimonas, Ruminococcus, and Mucispirillum were simultaneously significantly increased. The abundance of these bacteria was correlated to the expression levels of cytokines. Our findings suggest that the immunomodulatory activity of QDMC is partly mediated by the altered gut microbiota composition.
Collapse
Affiliation(s)
- Jinho An
- College of Pharmacy, Sahmyook University, Seoul 01795, Korea
| | - Heetae Lee
- College of Pharmacy, Sahmyook University, Seoul 01795, Korea
| | - Sungwon Lee
- College of Pharmacy, Sahmyook University, Seoul 01795, Korea
| | - Youngcheon Song
- College of Pharmacy, Sahmyook University, Seoul 01795, Korea
| | - Jiyeon Kim
- Climacteric Natural Products Research Institute, Sahmyook University, Seoul 01795, Korea
| | - Il Ho Park
- College of Pharmacy, Sahmyook University, Seoul 01795, Korea
| | - Hyunseok Kong
- Climacteric Natural Products Research Institute, Sahmyook University, Seoul 01795, Korea.,College of Animal Biotechnology and Resource, Sahmyook University, Seoul 01795, Korea
| | - Kyungjae Kim
- College of Pharmacy, Sahmyook University, Seoul 01795, Korea
| |
Collapse
|
11
|
Funosas G, Triadó-Margarit X, Castro F, Villafuerte R, Delibes-Mateos M, Rouco C, Casamayor EO. Individual fate and gut microbiome composition in the European wild rabbit (Oryctolagus cuniculus). Sci Rep 2021; 11:766. [PMID: 33436896 PMCID: PMC7804928 DOI: 10.1038/s41598-020-80782-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/30/2020] [Indexed: 01/12/2023] Open
Abstract
Studies connecting microbiome composition and functional performance in wildlife have received little attention and understanding their connections with wildlife physical condition are sorely needed. We studied the variation in gut microbiota (hard fecal pellets) between allopatric subspecies of the European wild rabbit in wild populations and in captured individuals studied under captivity. We evaluated the influence of environmental and host-specific factors. The microbiome of wild rabbit populations reduced its heterogeneity under controlled conditions. None of the host-specific factors tested correlated with the microbiota composition. We only observed significant intra-group dispersion for the age factor. The most diverse microbiomes were rich in Ruminococcaceae potentially holding an enriched functional profile with dominance of cellulases and xylanases, and suggesting higher efficiency in the digestion of fiber-rich food. Conversely, low diversity gut microbiomes showed dominance of Enterobacteriaceae potentially rich in amylases. We preliminary noticed geographical variations in field populations with higher dominance of Ruminococcaceae in south-western than in north-eastern Spain. Spatial differences appeared not to be subspecies driven, since they were lost in captivity, but environmentally driven, although differences in social structure and behavior may also play a role that deserve further investigations. A marginally significant relationship between the Ruminococcaceae/Enterobacteriaceae ratio and potential life expectancy was observed in captive rabbits. We hypothesize that the gut microbiome may determine the efficiency of feeding resource exploitation, and can also be a potential proxy for life expectancy, with potential applications for the management of declining wild herbivorous populations. Such hypotheses remain to be explored in the future.
Collapse
Affiliation(s)
- Gerard Funosas
- Microbial Community Ecology, Centre for Advanced Studies of Blanes-Spanish Council for Research CEAB-CSIC, Accés Cala St Francesc, 14, 17300, Blanes, Spain
| | - Xavier Triadó-Margarit
- Microbial Community Ecology, Centre for Advanced Studies of Blanes-Spanish Council for Research CEAB-CSIC, Accés Cala St Francesc, 14, 17300, Blanes, Spain
| | - Francisca Castro
- Departamento de Didácticas Específicas, Universidad de Córdoba, Sociedad, Ecología y Gestión del Medio Ambiente, UCO-IESA, Unidad Asociada al CSIC, 14004, Córdoba, Spain
| | - Rafael Villafuerte
- Institute of Advanced Social Studies-Spanish Council for Research (IESA-CSIC), 14004, Córdoba, Spain
| | - Miguel Delibes-Mateos
- Institute of Advanced Social Studies-Spanish Council for Research (IESA-CSIC), 14004, Córdoba, Spain
| | - Carlos Rouco
- Ecology Area, Faculty of Science, University of Cordoba, Sociedad, Ecología y Gestión del Medio Ambiente, UCO-IESA, Unidad Asociada al CSIC, 14071, Córdoba, Spain
| | - Emilio O Casamayor
- Microbial Community Ecology, Centre for Advanced Studies of Blanes-Spanish Council for Research CEAB-CSIC, Accés Cala St Francesc, 14, 17300, Blanes, Spain.
| |
Collapse
|
12
|
McLaren MR, Callahan BJ. Pathogen resistance may be the principal evolutionary advantage provided by the microbiome. Philos Trans R Soc Lond B Biol Sci 2020. [PMID: 32772671 DOI: 10.1098/rstb.2019.0592rstb20190592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023] Open
Abstract
To survive, plants and animals must continually defend against pathogenic microbes that would invade and disrupt their tissues. Yet they do not attempt to extirpate all microbes. Instead, they tolerate and even encourage the growth of commensal microbes, which compete with pathogens for resources and via direct inhibition. We argue that hosts have evolved to cooperate with commensals in order to enhance the pathogen resistance this competition provides. We briefly describe competition between commensals and pathogens within the host, consider how natural selection might favour hosts that tilt this competition in favour of commensals, and describe examples of extant host traits that may serve this purpose. Finally, we consider ways that this cooperative immunity may have facilitated the adaptive evolution of non-pathogen-related host traits. On the basis of these observations, we argue that pathogen resistance vies with other commensal-provided benefits for being the principal evolutionary advantage provided by the microbiome to host lineages across the tree of life. This article is part of the theme issue 'The role of the microbiome in host evolution'.
Collapse
Affiliation(s)
- Michael R McLaren
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC 27607, USA
| | - Benjamin J Callahan
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC 27607, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA
| |
Collapse
|
13
|
McLaren MR, Callahan BJ. Pathogen resistance may be the principal evolutionary advantage provided by the microbiome. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190592. [PMID: 32772671 PMCID: PMC7435163 DOI: 10.1098/rstb.2019.0592] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2020] [Indexed: 12/15/2022] Open
Abstract
To survive, plants and animals must continually defend against pathogenic microbes that would invade and disrupt their tissues. Yet they do not attempt to extirpate all microbes. Instead, they tolerate and even encourage the growth of commensal microbes, which compete with pathogens for resources and via direct inhibition. We argue that hosts have evolved to cooperate with commensals in order to enhance the pathogen resistance this competition provides. We briefly describe competition between commensals and pathogens within the host, consider how natural selection might favour hosts that tilt this competition in favour of commensals, and describe examples of extant host traits that may serve this purpose. Finally, we consider ways that this cooperative immunity may have facilitated the adaptive evolution of non-pathogen-related host traits. On the basis of these observations, we argue that pathogen resistance vies with other commensal-provided benefits for being the principal evolutionary advantage provided by the microbiome to host lineages across the tree of life. This article is part of the theme issue 'The role of the microbiome in host evolution'.
Collapse
Affiliation(s)
- Michael R. McLaren
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC 27607, USA
| | - Benjamin J. Callahan
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC 27607, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA
| |
Collapse
|
14
|
Xue Y, Lin L, Hu F, Zhu W, Mao S. Disruption of ruminal homeostasis by malnutrition involved in systemic ruminal microbiota-host interactions in a pregnant sheep model. MICROBIOME 2020; 8:138. [PMID: 32972462 PMCID: PMC7517653 DOI: 10.1186/s40168-020-00916-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 09/01/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Undernutrition is a prevalent and spontaneous condition in animal production which always affects microbiota-host interaction in gastrointestinal tract. However, how undernutrition affects crosstalk homeostasis is largely unknown. Here, we discover how undernutrition affects microbial profiles and subsequently how microbial metabolism affects the signal transduction and tissue renewal in ruminal epithelium, clarifying the detrimental effect of undernutrition on ruminal homeostasis in a pregnant sheep model. RESULTS Sixteen pregnant ewes (115 days of gestation) were randomly and equally assigned to the control (CON) and severe feed restriction (SFR) groups. Ewes on SFR treatment were restricted to a 30% level of ad libitum feed intake while the controls were fed normally. After 15 days, all ewes were slaughtered to collect ruminal digesta for 16S rRNA gene and metagenomic sequencing and ruminal epithelium for transcriptome sequencing. Results showed that SFR diminished the levels of ruminal volatile fatty acids and microbial proteins and repressed the length, width, and surface area of ruminal papillae. The 16S rRNA gene analysis indicated that SFR altered the relative abundance of ruminal bacterial community, showing decreased bacteria about saccharide degradation (Saccharofermentans and Ruminococcus) and propionate genesis (Succiniclasticum) but increased butyrate producers (Pseudobutyrivibrio and Papillibacter). Metagenome analysis displayed that genes related to amino acid metabolism, acetate genesis, and succinate-pathway propionate production were downregulated upon SFR, while genes involved in butyrate and methane genesis and acrylate-pathway propionate production were upregulated. Transcriptome and real-time PCR analysis of ruminal epithelium showed that downregulated collagen synthesis upon SFR lowered extracellular matrix-receptor interaction, inactivated JAK3-STAT2 signaling pathway, and inhibited DNA replication and cell cycle. CONCLUSIONS Generally, undernutrition altered rumen bacterial community and function profile to decrease ruminal energy retention, promoted epithelial glucose and fatty acid catabolism to elevate energy supply, and inhibited the proliferation of ruminal epithelial cells. These findings provide the first insight into the systemic microbiota-host interactions that are involved in disrupting the ruminal homeostasis under a malnutrition pattern. Video Abstract.
Collapse
Affiliation(s)
- Yanfeng Xue
- Centre for Ruminant Nutrition and Feed Technology Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
- National Center for International Research on Animal Gut Nutrition, National Experimental Teaching Demonstration Center of Animal Science, Nanjing Agricultural University, Nanjing, 210095 China
| | - Limei Lin
- Centre for Ruminant Nutrition and Feed Technology Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
- National Center for International Research on Animal Gut Nutrition, National Experimental Teaching Demonstration Center of Animal Science, Nanjing Agricultural University, Nanjing, 210095 China
| | - Fan Hu
- Centre for Ruminant Nutrition and Feed Technology Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
- National Center for International Research on Animal Gut Nutrition, National Experimental Teaching Demonstration Center of Animal Science, Nanjing Agricultural University, Nanjing, 210095 China
| | - Weiyun Zhu
- Centre for Ruminant Nutrition and Feed Technology Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
- National Center for International Research on Animal Gut Nutrition, National Experimental Teaching Demonstration Center of Animal Science, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shengyong Mao
- Centre for Ruminant Nutrition and Feed Technology Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 China
- National Center for International Research on Animal Gut Nutrition, National Experimental Teaching Demonstration Center of Animal Science, Nanjing Agricultural University, Nanjing, 210095 China
| |
Collapse
|
15
|
Influence of host genetics in shaping the rumen bacterial community in beef cattle. Sci Rep 2020; 10:15101. [PMID: 32934296 PMCID: PMC7493918 DOI: 10.1038/s41598-020-72011-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 08/19/2020] [Indexed: 01/04/2023] Open
Abstract
In light of recent host-microbial association studies, a consensus is evolving that species composition of the gastrointestinal microbiota is a polygenic trait governed by interactions between host genetic factors and the environment. Here, we investigated the effect of host genetic factors in shaping the bacterial species composition in the rumen by performing a genome-wide association study. Using a common set of 61,974 single-nucleotide polymorphisms found in cattle genomes (n = 586) and corresponding rumen bacterial community composition, we identified operational taxonomic units (OTUs), Families and Phyla with high heritability. The top associations (1-Mb windows) were located on 7 chromosomes. These regions were associated with the rumen microbiota in multiple ways; some (chromosome 19; position 3.0-4.0 Mb) are associated with closely related taxa (Prevotellaceae, Paraprevotellaceae, and RF16), some (chromosome 27; position 3.0-4.0 Mb) are associated with distantly related taxa (Prevotellaceae, Fibrobacteraceae, RF16, RFP12, S24-7, Lentisphaerae, and Tenericutes) and others (chromosome 23; position 0.0-1.0) associated with both related and unrelated taxa. The annotated genes associated with identified genomic regions suggest the associations observed are directed toward selective absorption of volatile fatty acids from the rumen to increase energy availability to the host. This study demonstrates that host genetics affects rumen bacterial community composition.
Collapse
|
16
|
Islam MR, Hassan YI, Das Q, Lepp D, Hernandez M, Godfrey DV, Orban S, Ross K, Delaquis P, Diarra MS. Dietary organic cranberry pomace influences multiple blood biochemical parameters and cecal microbiota in pasture-raised broiler chickens. J Funct Foods 2020. [DOI: 10.1016/j.jff.2020.104053] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
|
17
|
Tellez G, Arreguin-Nava MA, Maguey JA, Michel MA, Latorre JD, Merino-Guzman R, Hernandez-Velasco X, Moore PA, Hargis BM, Tellez-Isaias G. Effect of Bacillus-direct-fed microbial on leaky gut, serum peptide YY concentration, bone mineralization, and ammonia excretion in neonatal female turkey poults fed with a rye-based diet. Poult Sci 2020; 99:4514-4520. [PMID: 32867995 PMCID: PMC7598103 DOI: 10.1016/j.psj.2020.06.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 04/28/2020] [Accepted: 06/13/2020] [Indexed: 01/19/2023] Open
Abstract
Rye is high in nonstarch polysaccharides (NSP), a complex carbohydrate which cannot be digested by poultry as they lack the endogenous enzymes to do so. Exogenous carbohydrases must therefore be supplemented to avoid the antinutritional effects associated with a high NSP diet. The objectives of the present study were to evaluate the effects of a rye-based diet with and without supplementation of a Bacillus direct-fed microbial (DFM) on body weight, bone mineralization, and leaky gut, as well as its role on influencing serum concentrations of peptide YY (PPY) and the ammonia concentration in turkey manure. Two independent trials were conducted. In each experiment, day-of-hatch female turkey poults were neck tagged and randomly assigned to either a control rye-based diet or a rye-based diet supplemented with the DFM (n = 25 birds/group). At 10 days-of-age, poults in both groups were administered with an appropriate dose of fluorescein isothiocyanate-dextran (FITC-d) by oral gavage. One hour later, all poults were euthanized. Blood was collected to evaluate serum FITC-d and PPY concentrations. Furthermore, in Trial 2 only, both tibias were removed for assessment of bone parameters, and turkey manure was collected to evaluate physicochemical analysis. In both trials, poults treated with the DFM showed a significant increase (P < 0.05) in body weight and body weight gain as compared with control nontreated poults. Poults that received the DFM also had a significant reduction in serum levels of PPY and FITC-d when compared with control nontreated poults. In Trial 2, turkeys treated with the DFM had a substantial increase in tibia strength, tibia diameter, total ash, calcium, and phosphorus when compared with control nontreated turkeys. Their manure was also shown to have a significant reduction in the concentration of ammonia. This is the first report of a commercial DFM reducing the concentration of this compound in turkey manure. In summary, the results of the present study confirm that turkeys fed with a rye-based diet have a significant increase in gut permeability, a reduced body weight, and decreased bone mineralization when compared with turkeys fed with the DFM. Turkeys that received the rye-based diet supplemented with the Bacillus-DFM also had a significant reduction in the serum concentration of PPY when compared with control turkeys. This finding suggests a possible prebiotic effect of rye, warranting future studies to test this effect. Further studies to evaluate the microbiota diversity, as well as the concentration of ceca short-chain fatty acids, are also necessary to confirm the reliability of PPY as a potential metabolomic biomarker in poultry.
Collapse
Affiliation(s)
- G Tellez
- Department of Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA
| | | | - J A Maguey
- College of Superior Studies Cuautitlan, National Autonomous University of Mexico (UNAM), 54714, Mexico
| | - M A Michel
- College of Veterinary Medicine, National University of Nordeste, Corrientes, Argentina
| | - J D Latorre
- Department of Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA
| | - R Merino-Guzman
- Avian Medicine Department, College of Veterinary Medicine, UNAM, 04510, Mexico
| | - X Hernandez-Velasco
- Avian Medicine Department, College of Veterinary Medicine, UNAM, 04510, Mexico
| | - P A Moore
- USDA-ARS, Poultry Production and Product Safety Research Unit, University of Arkansas, Fayetteville, AR 72701, U.S.A
| | - B M Hargis
- Department of Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA
| | - G Tellez-Isaias
- Department of Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA.
| |
Collapse
|
18
|
Fitzgerald DM, Spence RJ, Stewart ZK, Prentis PJ, Sillence MN, de Laat MA. The effect of diet change and insulin dysregulation on the faecal microbiome of ponies. J Exp Biol 2020; 223:jeb219154. [PMID: 32098884 DOI: 10.1242/jeb.219154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/12/2020] [Indexed: 12/16/2022]
Abstract
The equine microbiome can change in response to dietary alteration and may play a role in insulin dysregulation. The aim of this study was to determine the effect of adding pasture to a hay diet on the faecal bacterial microbiome of both healthy and insulin-dysregulated ponies. Faecal samples were collected from 16 ponies before and after dietary change to enable bacterial 16S rRNA sequencing of the V3-V4 region. The dominant phyla in all samples were the Firmicutes and Bacteroidetes. The evenness of the bacterial populations decreased after grazing pasture, and when a pony was moderately insulin dysregulated (P=0.001). Evenness scores negatively correlated with post-prandial glucagon-like peptide-1 concentration after a hay-only diet (r²=-0.7, P=0.001). A change in diet explained 3% of faecal microbiome variability. We conclude that metabolically healthy ponies have greater microbial stability when challenged with a subtle dietary change, compared with moderately insulin-dysregulated ponies.
Collapse
Affiliation(s)
- Danielle M Fitzgerald
- Science and Engineering Faculty, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Robert J Spence
- Science and Engineering Faculty, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Zachary K Stewart
- Science and Engineering Faculty, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Peter J Prentis
- Science and Engineering Faculty, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Martin N Sillence
- Science and Engineering Faculty, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Melody A de Laat
- Science and Engineering Faculty, Queensland University of Technology, Brisbane, QLD 4001, Australia
| |
Collapse
|
19
|
Zhaxi Y, Meng X, Wang W, Wang L, He Z, Zhang X, Pu W. Duan-Nai-An, A Yeast Probiotic, Improves Intestinal Mucosa Integrity and Immune Function in Weaned Piglets. Sci Rep 2020; 10:4556. [PMID: 32165666 PMCID: PMC7067797 DOI: 10.1038/s41598-020-61279-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 02/20/2020] [Indexed: 12/01/2022] Open
Abstract
Post-weaning diarrhea commonly occurs in piglets and results in significant economic loss to swine producers. Non-antibiotic measures for managing post-weaning diarrhea are critically needed. Duan-Nai-An, a probiotic produced from the yeast fermentation of egg whites, was previously shown to optimize intestinal flora and reduce the incidence of clinical diarrhea in weaning piglets. To study the effects of Duan-Nai-An on mucosal integrity and immunity in pig intestine, we examined the microstructure and ultrastructure of the intestines of weaned pigs with or without Duan-Nai-An as a feed supplement. The piglets of the Duan-Nai-An-fed group developed intestines with intact columnar epithelia covered by tightly packed microvilli on the apical surface. However, piglets of the control group (no supplement) showed villous atrophy and thinning, microvillus slough, and in the severe cases, damage of intestinal epithelia and exposure of the underlying lamina propria. Moreover, piglets of the Duan-Nai-An-fed group showed apparent plasmocyte hyperplasia, increased lymphoid nodule numbers, well-developed Peyer's Patchs, and apparent germinal centers. The lymphoid tissues of the control group were far less developed, showing lymph node atrophy, lymphocyte reduction, degeneration, and necrosis. These results indicate that Duan-Nai-An improves the development of the intestinal structures and lymphoid tissues and promotes intestinal health in weaned piglets.
Collapse
Affiliation(s)
- Yingpai Zhaxi
- Key Laboratory of New Animal Drug Project, Gansu Province and Key Laboratory of Veterinary Pharmaceutics Discovery, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, 730050, China
- College of Life Sciences and Engineering, Northwest Minzu University, Lanzhou, 730030, China
| | - Xiaoqin Meng
- Lanzhou Center for Animal Disease Control and Prevention, Lanzhou, 730050, China
| | - Wenhui Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China
| | - Ling Wang
- Key Laboratory of New Animal Drug Project, Gansu Province and Key Laboratory of Veterinary Pharmaceutics Discovery, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, 730050, China
| | - Zhuolin He
- Key Laboratory of New Animal Drug Project, Gansu Province and Key Laboratory of Veterinary Pharmaceutics Discovery, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, 730050, China
| | - Xuejing Zhang
- Key Laboratory of New Animal Drug Project, Gansu Province and Key Laboratory of Veterinary Pharmaceutics Discovery, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, 730050, China
| | - Wanxia Pu
- Key Laboratory of New Animal Drug Project, Gansu Province and Key Laboratory of Veterinary Pharmaceutics Discovery, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, 730050, China.
| |
Collapse
|
20
|
Properties of hydrolyzed guar gum fermented in vitro with pig fecal inocula and its favorable impacts on microbiota. Carbohydr Polym 2020; 237:116116. [PMID: 32241396 DOI: 10.1016/j.carbpol.2020.116116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 02/12/2020] [Accepted: 03/02/2020] [Indexed: 01/02/2023]
Abstract
In order to identify an appropriate substitute for antibiotic use in livestock production, this study investigates the fermentation of guar gum and its low molecular weight hydrolyzed derivatives (GMLP-1, 1-10 kDa; GMLP-2, < 1 kDa) in pig fecal cultures and the associated effects on the intestinal microbiota. Both the non-hydrolyzed guar gum and GMLP were quickly utilized by fecal microbiota. GMLP-2 showed the most rapid SCFA-producing activity and produced higher concentrations of lactate, acetate, and propionate. However, GMLP-1 showed the highest yield of total SCFAs and butyrate. Both the guar gum and GMLP groups improved the abundance of Clostridium sensu stricto 1 and Bifidobacterium, but the most significant enhancement was observed with GMLP-1. This study showed that by associating with its chemical structure, GMLP-1 can be utilized to direct a targeted promotion of the intestinal microbiota and may offer the most favorable effects in livestock production.
Collapse
|
21
|
Quan J, Wu Z, Ye Y, Peng L, Wu J, Ruan D, Qiu Y, Ding R, Wang X, Zheng E, Cai G, Huang W, Yang J. Metagenomic Characterization of Intestinal Regions in Pigs With Contrasting Feed Efficiency. Front Microbiol 2020; 11:32. [PMID: 32038603 PMCID: PMC6989599 DOI: 10.3389/fmicb.2020.00032] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/09/2020] [Indexed: 11/13/2022] Open
Abstract
Greater feed efficiency (FE) is critical in increasing profitability while reducing the environmental impact of pig production. Previous studies that identified swine FE-associated bacterial taxa were limited in either sampling sites or sequencing methods. This study characterized the microbiomes within the intestine of FE contrasting Duroc × (Landrace × Yorkshire) (DLY) pigs with a comprehensive representation of diverse sampling sites (ileum, cecum, and colon) and a metagenomic sequencing approach. A total of 226 pigs were ranked according to their FE between weaning to 140 day old, and six with extreme phenotypes were selected, three for each of the high and low groups. The results revealed that the cecum and colon had similar microbial taxonomic composition and function, and had higher capacity in polysaccharide metabolism than the ileum. We found in cecum that the high FE pigs had slightly higher richness and evenness in their micriobiota than the low FE pigs. We identified 12 phyla, 17 genera, and 39 species (e.g., Treponema porcinum, Treponema bryantii, and Firmicutes bacterium CAG:110) that were potentially associated with swine FE variation in cecum microbiota through LEfSe analysis. Species enriched in the cecum of the high FE pigs had a greater ability to utilize dietary polysaccharides and dietary protein according to the KEGG annotation. Analysis of antibiotic resistance based on the CARD database annotation indicated that the macB resistant gene might play an important role in shaping the microbial community in the cecum of pigs with contrasting FE. The bacteria from the genus Prevotella was highly enriched in the cecum of low FE pigs, which may impair the establishment of a more effective nutrient harvesting microbiota because of the interaction between Prevotella and other benefical microbes. These findings improved our understanding of the microbial compositions in the different gut locations of DLY pigs and identified many biomarkers associated with FE variation wich may be used to develop strategies to improve FE in pigs.
Collapse
Affiliation(s)
- Jianping Quan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China.,Department of Animal Science, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, United States
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Yong Ye
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Longlong Peng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Jie Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Donglin Ruan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Yibin Qiu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Rongrong Ding
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Xingwang Wang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Wen Huang
- Department of Animal Science, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, United States
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| |
Collapse
|
22
|
Fu X, Liu Z, Zhu C, Mou H, Kong Q. Nondigestible carbohydrates, butyrate, and butyrate-producing bacteria. Crit Rev Food Sci Nutr 2018; 59:S130-S152. [PMID: 30580556 DOI: 10.1080/10408398.2018.1542587] [Citation(s) in RCA: 248] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Nondigestible carbohydrates (NDCs) are fermentation substrates in the colon after escaping digestion in the upper gastrointestinal tract. Among NDCs, resistant starch is not hydrolyzed by pancreatic amylases but can be degraded by enzymes produced by large intestinal bacteria, including clostridia, bacteroides, and bifidobacteria. Nonstarch polysaccharides, such as pectin, guar gum, alginate, arabinoxylan, and inulin fructans, and nondigestible oligosaccharides and their derivatives, can also be fermented by beneficial bacteria in the large intestine. Butyrate is one of the most important metabolites produced through gastrointestinal microbial fermentation and functions as a major energy source for colonocytes by directly affecting the growth and differentiation of colonocytes. Moreover, butyrate has various physiological effects, including enhancement of intestinal barrier function and mucosal immunity. In this review, several representative NDCs are introduced, and their chemical components, structures, and physiological functions, including promotion of the proliferation of butyrate-producing bacteria and enhancement of butyrate production, are discussed. We also describe the strategies for achieving directional accumulation of colonic butyrate based on endogenous generation mechanisms.
Collapse
Affiliation(s)
- Xiaodan Fu
- a College of Food Science and Engineering , Ocean University of China , Qingdao , China
| | - Zhemin Liu
- a College of Food Science and Engineering , Ocean University of China , Qingdao , China
| | - Changliang Zhu
- a College of Food Science and Engineering , Ocean University of China , Qingdao , China
| | - Haijin Mou
- a College of Food Science and Engineering , Ocean University of China , Qingdao , China
| | - Qing Kong
- a College of Food Science and Engineering , Ocean University of China , Qingdao , China
| |
Collapse
|
23
|
Sorini C, Cardoso RF, Gagliani N, Villablanca EJ. Commensal Bacteria-Specific CD4 + T Cell Responses in Health and Disease. Front Immunol 2018; 9:2667. [PMID: 30524431 PMCID: PMC6256970 DOI: 10.3389/fimmu.2018.02667] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/29/2018] [Indexed: 12/14/2022] Open
Abstract
Over the course of evolution, mammalian body surfaces have adapted their complex immune system to allow a harmless coexistence with the commensal microbiota. The adaptive immune response, in particular CD4+ T cell-mediated, is crucial to maintain intestinal immune homeostasis by discriminating between harmless (e.g., dietary compounds and intestinal microbes) and harmful stimuli (e.g., pathogens). To tolerate food molecules and microbial components, CD4+ T cells establish a finely tuned crosstalk with the environment whereas breakdown of these mechanisms might lead to chronic disease associated with mucosal barriers and beyond. How commensal-specific immune responses are regulated and how these molecular and cellular mechanisms can be manipulated to treat chronic disorders is yet poorly understood. In this review, we discuss current knowledge of the regulation of commensal bacteria-specific CD4+ T cells. We place particular focus on the key role of commensal-specific CD4+ T cells in maintaining tolerance while efficiently eradicating local and systemic infections, with a focus on factors that trigger their aberrant activation.
Collapse
Affiliation(s)
- Chiara Sorini
- Immunology and Allergy Unit, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
| | - Rebeca F. Cardoso
- Immunology and Allergy Unit, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
| | - Nicola Gagliani
- Immunology and Allergy Unit, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Eduardo J. Villablanca
- Immunology and Allergy Unit, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
| |
Collapse
|
24
|
Xu J, Li Y, Yang Z, Li C, Liang H, Wu Z, Pu W. Yeast Probiotics Shape the Gut Microbiome and Improve the Health of Early-Weaned Piglets. Front Microbiol 2018; 9:2011. [PMID: 30210480 PMCID: PMC6119770 DOI: 10.3389/fmicb.2018.02011] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 08/09/2018] [Indexed: 01/21/2023] Open
Abstract
Weaning is one of the most stressful challenges in the pig's life, which contributes to dysfunctions of intestinal and immune system, disrupts the gut microbial ecosystem, and therefore compromises the growth performance and health of piglets. To mitigate the negative impact of the stress on early-weaned piglets, effective measures are needed to promote gut health. Toward this end, we tamed a Saccharomyces cerevisiae strain and developed a probiotic Duan-Nai-An, which is a yeast culture of the tamed S. cerevisiae on egg white. In this study, we tested the performance of Duan-Nai-An on growth and health of early-weaned piglets and analyzed its impact on fecal microbiota. The results showed that Duan-Nai-An significantly improved weight gain and feed intake, and reduced diarrhea and death of early-weaned piglets. Analysis of the gut microbiota showed that the bacterial community was shaped by Duan-Nai-An and maintained as a relatively stable structure, represented by a higher core OTU number and lower unweighted UniFrac distances across the early weaned period. However, fungal community was not significantly shaped by the yeast probiotics. Notably, 13 bacterial genera were found to be associated with Duan-Nai-An feeding, including Enterococcus, Succinivibrio, Ruminococcus, Sharpea, Desulfovibrio, RFN20, Sphaerochaeta, Peptococcus, Anaeroplasma, and four other undefined genera. These findings suggest that Duan-Nai-An has the potential to be used as a feed supplement in swine production.
Collapse
Affiliation(s)
- Jinqiang Xu
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yuhui Li
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Zhiqiang Yang
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Chunhui Li
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hongyan Liang
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Zuowei Wu
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Wanxia Pu
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
| |
Collapse
|
25
|
Mayta-Apaza AC, Pottgen E, De Bodt J, Papp N, Marasini D, Howard L, Abranko L, Van de Wiele T, Lee SO, Carbonero F. Impact of tart cherries polyphenols on the human gut microbiota and phenolic metabolites in vitro and in vivo. J Nutr Biochem 2018; 59:160-172. [PMID: 30055451 DOI: 10.1016/j.jnutbio.2018.04.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 03/19/2018] [Accepted: 04/04/2018] [Indexed: 12/11/2022]
Abstract
Tart cherries have been reported to exert potential health benefits attributed to their specific and abundant polyphenol content. However, there is a need to study the impact and fate of tart cherries polyphenols in the gut microbiota. Here, tart cherries, pure polyphenols (and apricots) were submitted to in vitro bacterial fermentation assays and assessed through 16S rRNA gene sequence sequencing and metabolomics. A short-term (5 days, 8 oz. daily) human dietary intervention study was also conducted for microbiota analyses. Tart cherry concentrate juices were found to contain expected abundances of anthocyanins (cyanidin-glycosylrutinoside) and flavonoids (quercetin-rutinoside) and high amounts of chlorogenic and neochlorogenic acids. Targeted metabolomics confirmed that gut microbes were able to degrade those polyphenols mainly to 4-hydroxyphenylpropionic acids and to lower amounts of epicatechin and 4-hydroxybenzoic acids. Tart cherries were found to induce a large increase of Bacteroides in vitro, likely due to the input of polysaccharides, but prebiotic effect was also suggested by Bifidobacterium increase from chlorogenic acid. In the human study, two distinct and inverse responses to tart cherry consumption were associated with initial levels of Bacteroides. High-Bacteroides individuals responded with a decrease in Bacteroides and Bifidobacterium, and an increase of Lachnospiraceae, Ruminococcus and Collinsella. Low-Bacteroides individuals responded with an increase in Bacteroides or Prevotella and Bifidobacterium, and a decrease of Lachnospiraceae, Ruminococcus and Collinsella. These data confirm that gut microbiota metabolism, in particular the potential existence of different metabotypes, needs to be considered in studies attempting to link tart cherries consumption and health.
Collapse
Affiliation(s)
| | - Ellen Pottgen
- Food Science, University of Arkansas, Fayetteville, AR, United States
| | - Jana De Bodt
- Laboratory of Microbial Ecology and Technology (LabMET), Faculty of BioScience Engineering, Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Nora Papp
- Faculty of Food Science, Department of Applied Chemistry, Szent István University, 1118 Budapest, Hungary
| | - Daya Marasini
- Food Science, University of Arkansas, Fayetteville, AR, United States
| | - Luke Howard
- Food Science, University of Arkansas, Fayetteville, AR, United States
| | - Laszlo Abranko
- Faculty of Food Science, Department of Applied Chemistry, Szent István University, 1118 Budapest, Hungary
| | - Tom Van de Wiele
- Laboratory of Microbial Ecology and Technology (LabMET), Faculty of BioScience Engineering, Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Sun-Ok Lee
- Food Science, University of Arkansas, Fayetteville, AR, United States; Center for Human Nutrition, Division of Agriculture, University of Arkansas, United States
| | - Franck Carbonero
- Food Science, University of Arkansas, Fayetteville, AR, United States; Center for Human Nutrition, Division of Agriculture, University of Arkansas, United States.
| |
Collapse
|
26
|
Curtis JT, Assefa S, Francis A, Köhler GA. Fecal microbiota in the female prairie vole (Microtus ochrogaster). PLoS One 2018; 13:e0190648. [PMID: 29579049 PMCID: PMC5868765 DOI: 10.1371/journal.pone.0190648] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 12/18/2017] [Indexed: 12/15/2022] Open
Abstract
We examined the fecal microbiota of female prairie voles. This species is socially and, likely, sexually monogamous, and thus serves as a valuable model in which to examine the interaction between the microbiota-gut-brain axis and social behavior. At present, little is known about the gastrointestinal microbiota of prairie voles; therefore, we performed a first characterization of the fecal microbiota using 16S rRNA gene amplicon sequencing. Semiconductor sequencing technology on an Ion Torrent PGM platform was used to assess the composition of fecal microbiotas from twelve female prairie voles. Following quality filtering, 1,017,756 sequencing reads were classified from phylum to genus level. At the phylum level, Firmicutes, Bacteroidetes, and Saccharibacteria were the predominant taxa, while the Bacteriodales, Erysipelotrichaceae, Ruminococcaceae, and Lachnospiraceae contributed the most dominant microbial groups and genera. Microbial community membership was most similar between vole sibling pairs, but consideration of taxon abundances weakened these associations. The interdependence of host factors such as genetics and behavior with the gastrointestinal microbiota is likely to be particularly pronounced in prairie voles. Our pilot characterization of the prairie vole intestinal microbiota revealed a microbial community composition remarkably consistent with the monogastric alimentary system of these rodents and their diet rich in complex plant carbohydrates. The highly social nature of these animals poses specific challenges to microbiome analyses that nonetheless are valuable for advancing research on the microbiota-gut-brain-behavior axis. Our study provides an important basis for future microbiome research in this emerging model organism for studying social behavior.
Collapse
Affiliation(s)
- J. Thomas Curtis
- Department of Pharmacology and Physiology, Oklahoma State University Center for Health Sciences, Tulsa, Oklahoma, United States of America
| | - Senait Assefa
- Department of Biochemistry and Microbiology, Oklahoma State University Center for Health Sciences, Tulsa, Oklahoma, United States of America
| | - Amie Francis
- Department of Pharmacology and Physiology, Oklahoma State University Center for Health Sciences, Tulsa, Oklahoma, United States of America
| | - Gerwald A. Köhler
- Department of Biochemistry and Microbiology, Oklahoma State University Center for Health Sciences, Tulsa, Oklahoma, United States of America
- * E-mail:
| |
Collapse
|
27
|
Kedia S, Rampal R, Paul J, Ahuja V. Gut microbiome diversity in acute infective and chronic inflammatory gastrointestinal diseases in North India. J Gastroenterol 2016; 51:660-71. [PMID: 26994772 DOI: 10.1007/s00535-016-1193-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 02/23/2016] [Indexed: 02/04/2023]
Abstract
The disease profile in the Indian population provides a unique opportunity for studying the host microbiome interaction in both infectious (amebiasis) and autoimmune diseases like inflammatory bowel disease (IBD) from a similar environment and genetic background. Analysis of fecal samples from untreated amebic liver abscess (ALA) patients, Entamoeba histolytica (Eh)-negative and -positive asymptomatic individuals, and pus samples from naive ALA patients revealed a significant reduction in Lactobacillus in asymptomatic individuals (Eh +ve) and ALA patients. Two anaerobic genera, namely Bacteroides and Peptostreptococcus, were detected in naive ALA pus samples. Analysis of fecal samples from amoebic colitis patients showed a significant decline in population of Bacteroides, Clostridium coccoides and leptum subgroup, Lactobacillus, Campylobacter, and Eubacterium, whereas a significant increase in Bifidobacterium was observed. Mucosa-associated bacterial flora analysis from IBD patients and healthy controls revealed a significant difference in concentration of bacteria among predominating and subdominating genera between ulcerative colitis (UC), Crohn's disease (CD) patients, and controls. In contrast to the mucosal studies, we found a significant increase in lactobacilli population in fecal samples of active UC patients. Another study revealed a significant decrease of Clostridium coccoides and leptum clusters in fecal samples of active UC patients along with decreased concentrations of fecal SCFAs, especially of n-butyrate, iso-butyrate, and acetate. We therefore found similar perturbations in gut microbiome in both infectious and autoimmune diseases, indicating inflammation to be the major driver for changes in gut microbiome.
Collapse
Affiliation(s)
- Saurabh Kedia
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Ritika Rampal
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Jaishree Paul
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Vineet Ahuja
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India.
| |
Collapse
|
28
|
Grandeur Alliances: Symbiont Metabolic Integration and Obligate Arthropod Hematophagy. Trends Parasitol 2016; 32:739-749. [PMID: 27236581 DOI: 10.1016/j.pt.2016.05.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/05/2016] [Accepted: 05/06/2016] [Indexed: 01/15/2023]
Abstract
Several arthropod taxa live exclusively on vertebrate blood. This food source lacks essential metabolites required for the maintenance of metabolic homeostasis, and as such, these arthropods have formed symbioses with nutrient-supplementing microbes that facilitate their host's 'hematophagous' feeding ecology. Herein we highlight metabolic contributions of bacterial symbionts that reside within tsetse flies, bed bugs, lice, reduviid bugs, and ticks, with specific emphasis on B vitamin and cofactor biosynthesis. Importantly, these arthropods can transmit pathogens of medical and veterinary relevance and/or cause infestations that induce psychological and dermatological distress. Microbial metabolites, and the biochemical pathways that generate them, can serve as specific targets of novel control mechanisms aimed at disrupting the metabolism of hematophagous arthropods, thus combatting pest invasion and vector-borne pathogen transmission.
Collapse
|
29
|
Selak M, Rivière A, Moens F, Van den Abbeele P, Geirnaert A, Rogelj I, Leroy F, De Vuyst L. Inulin-type fructan fermentation by bifidobacteria depends on the strain rather than the species and region in the human intestine. Appl Microbiol Biotechnol 2016; 100:4097-107. [PMID: 26861055 DOI: 10.1007/s00253-016-7351-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 01/08/2016] [Accepted: 01/23/2016] [Indexed: 01/01/2023]
Abstract
Inulin-type fructans (ITF) are known to cause a health-promoting bifidogenic effect, although the ITF degradation capacity of bifidobacteria in different intestinal regions remains unclear. The present study aims at offering new insights into this link, making use of a collection of 190 bifidobacterial strains, encompassing strains from gut biopsies (terminal ileum and proximal colon; mucosa-associated strains) and the simulator of the human intestinal microbial ecosystem (SHIME®; proximal and distal colon vessels; lumen-associated strains). A multivariate data analysis of all fermentation data revealed four clusters corresponding with different types of ITF degradation fingerprints, which were not correlated with the region in the intestine, suggesting that the degradation of ITF is uniform along the human intestine. Strains from cluster 1 consumed fructose, while strains from cluster 2 consumed more oligofructose than fructose. Higher fructose and oligofructose consumption was characteristic for clusters 3 and 4 strains, which degraded inulin too. In general, the mucosa-associated strains from biopsy origin seemed to be more specialized in the consumption of fructose and oligofructose, while the lumen-associated strains from SHIME origin displayed a higher degradation degree of inulin. Further, intra-species variability in ITF degradation was found, indicating strain-specific variations. The coexistence of different bifidobacterial strains with different ITF degradation fingerprints within the same intestinal region suggests cooperation for the degradation of ITF, with opportunities for cross-feeding on strain and/or species level.
Collapse
Affiliation(s)
- Marija Selak
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
| | - Audrey Rivière
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
| | - Frédéric Moens
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
| | - Pieter Van den Abbeele
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000, Ghent, Belgium
| | - Annelies Geirnaert
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000, Ghent, Belgium
| | - Irena Rogelj
- Institute of Dairy Science and Probiotics, Biotechnical Faculty, University of Ljubljana, Groblje 3, 1230, Domžale, Slovenia
| | - Frédéric Leroy
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium.
| |
Collapse
|
30
|
Munns KD, Selinger LB, Stanford K, Guan L, Callaway TR, McAllister TA. Perspectives on super-shedding of Escherichia coli O157:H7 by cattle. Foodborne Pathog Dis 2014; 12:89-103. [PMID: 25514549 DOI: 10.1089/fpd.2014.1829] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli O157:H7 is a foodborne pathogen that causes illness in humans worldwide. Cattle are the primary reservoir of this bacterium, with the concentration and frequency of E. coli O157:H7 shedding varying greatly among individuals. The term "super-shedder" has been applied to cattle that shed concentrations of E. coli O157:H7 ≥ 10⁴ colony-forming units/g feces. Super-shedders have been reported to have a substantial impact on the prevalence and transmission of E. coli O157:H7 in the environment. The specific factors responsible for super-shedding are unknown, but are presumably mediated by characteristics of the bacterium, animal host, and environment. Super-shedding is sporadic and inconsistent, suggesting that biofilms of E. coli O157:H7 colonizing the intestinal epithelium in cattle are intermittently released into feces. Phenotypic and genotypic differences have been noted in E. coli O157:H7 recovered from super-shedders as compared to low-shedding cattle, including differences in phage type (PT21/28), carbon utilization, degree of clonal relatedness, tir polymorphisms, and differences in the presence of stx2a and stx2c, as well as antiterminator Q gene alleles. There is also some evidence to support that the native fecal microbiome is distinct between super-shedders and low-shedders and that low-shedders have higher levels of lytic phage within feces. Consequently, conditions within the host may determine whether E. coli O157:H7 can proliferate sufficiently for the host to obtain super-shedding status. Targeting super-shedders for mitigation of E. coli O157:H7 has been proposed as a means of reducing the incidence and spread of this pathogen to the environment. If super-shedders could be easily identified, strategies such as bacteriophage therapy, probiotics, vaccination, or dietary inclusion of plant secondary compounds could be specifically targeted at this subpopulation. Evidence that super-shedder isolates share a commonality with isolates linked to human illness makes it imperative that the etiology of this phenomenon be characterized.
Collapse
Affiliation(s)
- Krysty D Munns
- 1 Agriculture and Agri-Food Canada, Lethbridge Research Centre , Lethbridge, Alberta, Canada
| | | | | | | | | | | |
Collapse
|
31
|
De Vuyst L, Moens F, Selak M, Rivière A, Leroy F. Summer Meeting 2013: growth and physiology of bifidobacteria. J Appl Microbiol 2013; 116:477-91. [PMID: 24314205 DOI: 10.1111/jam.12415] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 11/15/2013] [Accepted: 11/22/2013] [Indexed: 01/11/2023]
Abstract
Bifidobacteria are a minor fraction of the human colon microbiota with interesting properties for carbohydrate degradation. Monosaccharides such as glucose and fructose are degraded through the bifid shunt, a dedicated pathway involving phosphoketolase activity. Its stoechiometry learns that three moles of acetate and two moles of lactate are produced per two moles of glucose or fructose that are degraded. However, deviations from this 3 : 2 ratio occur, depending on the rate of substrate consumption. Slower growth rates favour the production of acetate and pyruvate catabolites (such as formate) at the cost of lactate. Interestingly, bifidobacteria are capable to degrade inulin-type fructans (ITF) (oligofructose and inulin) and arabinoxylan-oligosaccharides (AXOS). Beta-fructofuranosidase activity enables bifidobacteria to degrade ITF. However, this property is strain-dependent. Some strains consume both fructose and oligofructose, with different preferences and degradation rates. Small oligosaccharides (degree of polymerization or DP of 2-7) are taken up, in a sequential order, indicating intracellular degradation and as such giving these bacteria a competitive advantage towards other inulin-type fructan degraders such as lactobacilli, bacteroides and roseburias. Other strains consume long fractions of oligofructose and inulin. Exceptionally, oligosaccharides with a DP of up to 20 (long-chain inulin) are consumed by specific strains. Also, the degradation of AXOS by α-arabinofuranosidase and β-xylosidase is strain-dependent. Particular strains consume the arabinose substituents, whether or not together with a consumption of the xylose backbones of AXOS, either up to xylotetraose or higher and either extra- or intracellularly. The production of high amounts of acetate that accompanies inulin-type fructan degradation by bifidobacteria cross-feeds other colon bacteria involved in the production of butyrate. However, bifidobacterial strain-dependent differences in prebiotic degradation indicate the existence of niche-specific adaptations and hence mechanisms to avoid competition among each other and to favour coexistence with other colon bacteria.
Collapse
Affiliation(s)
- L De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Vrije Universiteit Brussel, Brussels, Belgium
| | | | | | | | | |
Collapse
|
32
|
The ability of bifidobacteria to degrade arabinoxylan oligosaccharide constituents and derived oligosaccharides is strain dependent. Appl Environ Microbiol 2013; 80:204-17. [PMID: 24141124 DOI: 10.1128/aem.02853-13] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Arabinoxylan oligosaccharides (AXOS) are prebiotic carbohydrates with promising health-promoting properties that stimulate the activity of specific colon bacteria, in particular bifidobacteria. However, the mechanisms by which bifidobacterial strains break down these compounds in the colon is still unknown. This study investigates AXOS consumption of a large number of bifidobacterial strains (36), belonging to 11 different species, systematically. To determine their degradation mechanisms, all strains were grown on a mixture of arabinose and xylose, xylo-oligosaccharides, and complex AXOS molecules as the sole added energy sources. Based on principal component and cluster analyses of their different arabinose substituent and/or xylose backbone consumption patterns, five clusters that were species independent could be distinguished among the bifidobacterial strains tested. In parallel, the strains were screened for the presence of genes encoding several putative AXOS-degrading enzymes, but no clear-cut correlation could be made with the different degradation mechanisms. The intra- and interspecies differences in the consumption patterns of AXOS indicate that bifidobacterial strains could avoid competition among each other or even could cooperate jointly to degrade these complex prebiotics. The knowledge gained on the AXOS degradation mechanisms in bifidobacteria can be of importance in the rational design of prebiotics with tailor-made composition and thus increased specificity in the colon.
Collapse
|
33
|
He X, Marco ML, Slupsky CM. Emerging aspects of food and nutrition on gut microbiota. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:9559-9574. [PMID: 24028159 DOI: 10.1021/jf4029046] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The human gastrointestinal tract contains a highly complex ecosystem that harbors various microorganisms, which together create a unique environment within each individual. There is growing awareness that dietary habits are one of the essential factors contributing to the microbial diversity and community configuration that ultimately affects human health. From an evolutionary perspective, human dietary history can be viewed as a central factor in the selection of the gut microbial community and stabilization of the mutualistic host-microbial interaction, that together drive host phenotype. Herein, current knowledge concerning the influence of major dietary macrostructure and individual food ingredients is presented. This knowledge will provide perspectives for personalized gut microbiota management and, ultimately, movement toward an era of personalized nutrition and medicine.
Collapse
Affiliation(s)
- Xuan He
- Department of Nutrition and ‡Department of Food Science and Technology, University of California , Davis, California 95616, United States
| | | | | |
Collapse
|
34
|
Lettat A, Benchaar C. Diet-induced alterations in total and metabolically active microbes within the rumen of dairy cows. PLoS One 2013; 8:e60978. [PMID: 23593365 PMCID: PMC3622600 DOI: 10.1371/journal.pone.0060978] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 03/05/2013] [Indexed: 12/13/2022] Open
Abstract
DNA-based techniques are widely used to study microbial populations; however, this approach is not specific to active microbes, because DNA may originate from inactive and/or dead cells. Using cDNA and DNA, respectively, we aimed to discriminate the active microbes from the total microbial community within the rumen of dairy cows fed diets with increasing proportions of corn silage (CS). Nine multiparous lactating Holstein cows fitted with ruminal cannulas were used in a replicated 3×3 Latin square (32-d period; 21-d adaptation) design to investigate diet-induced shifts in microbial populations by targeting the rDNA gene. Cows were fed a total mixed ration with the forage portion being either barley silage (0% CS), a 50∶50 mixture of barley silage and corn silage (50% CS), or corn silage (100% CS). No differences were found for total microbes analyzed by quantitative PCR, but changes were observed within the active ones. Feeding more CS to dairy cows was accompanied by an increase in Prevotella rRNA transcripts (P = 0.10) and a decrease in the protozoal rRNA transcripts (P<0.05). Although they were distributed differently among diets, 78% of the amplicons detected in DNA- and cDNA-based fingerprints were common to total and active bacterial communities. These may represent a bacterial core of abundant and active cells that drive the fermentation processes. In contrast, 10% of amplicons were specific to total bacteria and may represent inactive or dead cells, whereas 12% were only found within the active bacterial community and may constitute slow-growing bacteria with high metabolic activity. It appears that cDNA-based analysis is more discriminative to identify diet-induced shifts within the microbial community. This approach allows the detection of diet-induced changes in the microbial populations as well as particular bacterial amplicons that remained undetected using DNA-based methods.
Collapse
Affiliation(s)
- Abderzak Lettat
- Agriculture and Agri-Food Canada, Dairy and Swine Research and Development Centre, Sherbrooke, Quebec, Canada
| | - Chaouki Benchaar
- Agriculture and Agri-Food Canada, Dairy and Swine Research and Development Centre, Sherbrooke, Quebec, Canada
- * E-mail:
| |
Collapse
|
35
|
Muegge BD, Kuczynski J, Knights D, Clemente JC, González A, Fontana L, Henrissat B, Knight R, Gordon JI. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 2011; 332:970-4. [PMID: 21596990 PMCID: PMC3303602 DOI: 10.1126/science.1198719] [Citation(s) in RCA: 1280] [Impact Index Per Article: 98.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Coevolution of mammals and their gut microbiota has profoundly affected their radiation into myriad habitats. We used shotgun sequencing of microbial community DNA and targeted sequencing of bacterial 16S ribosomal RNA genes to gain an understanding of how microbial communities adapt to extremes of diet. We sampled fecal DNA from 33 mammalian species and 18 humans who kept detailed diet records, and we found that the adaptation of the microbiota to diet is similar across different mammalian lineages. Functional repertoires of microbiome genes, such as those encoding carbohydrate-active enzymes and proteases, can be predicted from bacterial species assemblages. These results illustrate the value of characterizing vertebrate gut microbiomes to understand host evolutionary histories at a supraorganismal level.
Collapse
Affiliation(s)
- Brian D. Muegge
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Justin Kuczynski
- Department of Molecular, Cellular and Developmental Biology, Univ. of Colorado, Boulder, CO 80309, USA
| | - Dan Knights
- Department of Computer Science, Univ. of Colorado, Boulder, CO 80309, USA
| | - Jose C. Clemente
- Department of Computer Science, Univ. of Colorado, Boulder, CO 80309, USA
| | - Antonio González
- Department of Computer Science, Univ. of Colorado, Boulder, CO 80309, USA
| | - Luigi Fontana
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63108, USA
- Division of Nutrition and Aging, Istituto Superiore di Sanità, Rome, Italy
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Universities, Marseille, France
| | - Rob Knight
- HHMI and Department of Chemistry and Biochemistry, Univ. of Colorado, Boulder, CO 80309, USA
| | - Jeffrey I. Gordon
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
- To whom correspondence should be sent:
| |
Collapse
|
36
|
In-vitro assessment of the effects of dietary fibers on microbial fermentation and communities from large intestinal digesta of pigs. Food Hydrocoll 2011. [DOI: 10.1016/j.foodhyd.2010.02.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
37
|
In vitro kinetics of prebiotic inulin-type fructan fermentation by butyrate-producing colon bacteria: implementation of online gas chromatography for quantitative analysis of carbon dioxide and hydrogen gas production. Appl Environ Microbiol 2009; 75:5884-92. [PMID: 19633122 DOI: 10.1128/aem.00876-09] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Kinetic analyses of bacterial growth, carbohydrate consumption, and metabolite production of five butyrate-producing clostridial cluster XIVa colon bacteria grown on acetate plus fructose, oligofructose, inulin, or lactate were performed. A gas chromatography method was set up to assess H2 and CO2 production online and to ensure complete coverage of all metabolites produced. Method accuracy was confirmed through the calculation of electron and carbon recoveries. Fermentations with Anaerostipes caccae DSM 14662(T), Roseburia faecis DSM 16840(T), Roseburia hominis DSM 16839(T), and Roseburia intestinalis DSM 14610(T) revealed similar patterns of metabolite production with butyrate, CO2, and H2 as the main metabolites. R. faecis DSM 16840(T) and R. intestinalis DSM 14610(T) were able to degrade oligofructose, displaying a nonpreferential breakdown mechanism. Lactate consumption was only observed with A. caccae DSM 14662(T). Roseburia inulinivorans DSM 16841(T) was the only strain included in the present study that was able to grow on fructose, oligofructose, and inulin. The metabolites produced were lactate, butyrate, and CO2, without H2 production, indicating an energy metabolism distinct from that of other Roseburia species. Oligofructose degradation was nonpreferential. In a coculture of R. inulinivorans DSM 16841(T) with the highly competitive strain Bifidobacterium longum subsp. longum LMG 11047 on inulin, hardly any production of butyrate and CO2 was detected, indicating a lack of competitiveness of the butyrate producer. Complete recovery of metabolites during fermentations of clostridial cluster XIVa butyrate-producing colon bacteria allowed stoichiometric balancing of the metabolic pathway for butyrate production, including H2 formation.
Collapse
|
38
|
Flint HJ, Bayer EA. Plant cell wall breakdown by anaerobic microorganisms from the Mammalian digestive tract. Ann N Y Acad Sci 2008; 1125:280-8. [PMID: 18378598 DOI: 10.1196/annals.1419.022] [Citation(s) in RCA: 151] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Degradation of lignocellulosic plant material in the mammalian digestive tract is accomplished by communities of anaerobic microorganisms that exist in symbiotic association with the host. Catalytic domains and substrate-binding modules concerned with plant polysaccharide degradation are found in a variety of anaerobic bacteria, fungi, and protozoa from the mammalian gut. The organization of plant cell wall-degrading enzymes, however, varies widely. The cellulolytic gram-positive bacterium Ruminococcus flavefaciens produces an elaborate cellulosomal enzyme complex that is anchored to the bacterial cell wall; assembly of the complex involves at least five different dockerin:cohesin specificities, and the R. flavefaciens genome encodes at least 180 dockerin-containing proteins that encompass a wide array of catalytic and binding activities. On the other hand, in the cellulolytic protozoan, Polyplastron multivesiculatum, individual plant cell wall-degrading enzymes appear to be secreted into food vacuoles, while the gram-negative bacterium Prevotella bryantii appears to possess a sequestration-type system for the utilization of soluble xylans. The system that is employed for polysaccharide utilization must play a major role in defining the ecological niche that each organism occupies within a complex gut community. 16S rRNA analyses are also revealing uncultured bacterial species closely adherent to fibrous substrates in the rumen and in the large intestine of animals and humans. The true complexity, both at a single organism and community level, of the microbial enzyme systems that allow animals to digest plant material is beginning to become apparent.
Collapse
Affiliation(s)
- Harry J Flint
- Microbial Ecology Group, Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK.
| | | |
Collapse
|
39
|
Dowd SE, Sun Y, Wolcott RD, Domingo A, Carroll JA. Bacterial Tag–Encoded FLX Amplicon Pyrosequencing (bTEFAP) for Microbiome Studies: Bacterial Diversity in the Ileum of Newly WeanedSalmonella-Infected Pigs. Foodborne Pathog Dis 2008; 5:459-72. [DOI: 10.1089/fpd.2008.0107] [Citation(s) in RCA: 331] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Scot E. Dowd
- USDA-ARS Livestock Issues Research Unit, Lubbock, Texas
| | - Yan Sun
- Medical Biofilm Research Institute, Lubbock, Texas
| | | | | | | |
Collapse
|
40
|
Dowd SE, Callaway TR, Wolcott RD, Sun Y, McKeehan T, Hagevoort RG, Edrington TS. Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). BMC Microbiol 2008; 8:125. [PMID: 18652685 PMCID: PMC2515157 DOI: 10.1186/1471-2180-8-125] [Citation(s) in RCA: 756] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2008] [Accepted: 07/24/2008] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The microbiota of an animal's intestinal tract plays important roles in the animal's overall health, productivity and well-being. There is still a scarcity of information on the microbial diversity in the gut of livestock species such as cattle. The primary reason for this lack of data relates to the expense of methods needed to generate such data. Here we have utilized a bacterial tag-encoded FLX 16s rDNA amplicon pyrosequencing (bTEFAP) approach that is able to perform diversity analyses of gastrointestinal populations. bTEFAP is relatively inexpensive in terms of both time and labor due to the implementation of a novel tag priming method and an efficient bioinformatics pipeline. We have evaluated the microbiome from the feces of 20 commercial, lactating dairy cows. RESULTS Ubiquitous bacteria detected from the cattle feces included Clostridium, Bacteroides, Porpyhyromonas, Ruminococcus, Alistipes, Lachnospiraceae, Prevotella, Lachnospira, Enterococcus, Oscillospira, Cytophage, Anaerotruncus, and Acidaminococcus spp. Foodborne pathogenic bacteria were detected in several of the cattle, a total of 4 cows were found to be positive for Salmonella spp (tentative enterica) and 6 cows were positive for Campylobacter spp. (tentative lanienae). CONCLUSION Using bTEFAP we have examined the microbiota in the feces of cattle. As these methods continue to mature we will better understand the ecology of the major populations of bacteria the lower intestinal tract. This in turn will allow for a better understanding of ways in which the intestinal microbiome contributes to animal health, productivity and wellbeing.
Collapse
Affiliation(s)
- Scot E Dowd
- USDA-ARS Livestock Issues Research Unit, Lubbock, TX 79403, USA.
| | | | | | | | | | | | | |
Collapse
|
41
|
Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Nat Rev Microbiol 2008; 6:121-31. [PMID: 18180751 DOI: 10.1038/nrmicro1817] [Citation(s) in RCA: 1081] [Impact Index Per Article: 67.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The microbiota of the mammalian intestine depend largely on dietary polysaccharides as energy sources. Most of these polymers are not degradable by the host, but herbivores can derive 70% of their energy intake from microbial breakdown--a classic example of mutualism. Moreover, dietary polysaccharides that reach the human large intestine have a major impact on gut microbial ecology and health. Insight into the molecular mechanisms by which different gut bacteria use polysaccharides is, therefore, of fundamental importance. Genomic analyses of the gut microbiota could revolutionize our understanding of these mechanisms and provide new biotechnological tools for the conversion of polysaccharides, including lignocellulosic biomass, into monosaccharides.
Collapse
|
42
|
Abstract
The microbial communities of humans are characteristic and complex mixtures of microorganisms that have co-evolved with their human hosts. The species that make up these communities vary between hosts as a result of restricted migration of microorganisms between hosts and strong ecological interactions within hosts, as well as host variability in terms of diet, genotype and colonization history. The shared evolutionary fate of humans and their symbiotic bacteria has selected for mutualistic interactions that are essential for human health, and ecological or genetic changes that uncouple this shared fate can result in disease. In this way, looking to ecological and evolutionary principles might provide new strategies for restoring and maintaining human health.
Collapse
|
43
|
Flint HJ, Duncan SH, Scott KP, Louis P. Interactions and competition within the microbial community of the human colon: links between diet and health. Environ Microbiol 2007; 9:1101-11. [PMID: 17472627 DOI: 10.1111/j.1462-2920.2007.01281.x] [Citation(s) in RCA: 395] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The microbiota of the human intestinal tract play an important role in health, in particular by mediating many of the effects of diet upon gut health. Surveys of 16S rRNA sequence diversity in the human colon have emphasized the low proportion of sequences that match cultured bacterial species. This may reflect limited recent effort on cultivation rather than inherent unculturability, however, as anaerobic isolation methods can apparently recover a wide range of the diversity found. A combination of information from representative cultures, molecular tools for enumeration and tracking of bacterial metabolites offers the most powerful route to understanding the roles played by different groups of bacteria in the gut ecosystem. Progress is being made for example in defining key functional groups including primary colonizers of insoluble dietary substrates, and major contributors to metabolites such as butyrate that influence the health of the gut mucosa. There is increasing evidence that bacterial populations in the large intestine respond to changes in diet, in particular to the type and quantity of dietary carbohydrate. A general consequence of increased carbohydrate consumption is to reduce the pH of the gut lumen, which is likely to play a major role in determining bacterial metabolism and competition. Oligosaccharides used as dietary prebiotics must inevitably have complex effects upon the bacterial community that include non-target organisms and the consequences of metabolic cross-feeding and changes in the gut environment.
Collapse
Affiliation(s)
- Harry J Flint
- Microbial Ecology Group, Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB219SB, UK.
| | | | | | | |
Collapse
|
44
|
Leitch ECM, Walker AW, Duncan SH, Holtrop G, Flint HJ. Selective colonization of insoluble substrates by human faecal bacteria. Environ Microbiol 2007; 9:667-79. [PMID: 17298367 DOI: 10.1111/j.1462-2920.2006.01186.x] [Citation(s) in RCA: 199] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Insoluble plant polysaccharides and endogenous mucin are important energy sources for human colonic microorganisms. The object of this study was to determine whether or not specific communities colonize these substrates. Using faecal samples from four individuals as inocula for an anaerobic in vitro continuous flow system, the colonization of wheat bran, high amylose starch and porcine gastric mucin was examined. Recovered substrates were extensively washed and the remaining tightly attached bacterial communities were identified using polymerase chain reaction-amplified 16S rRNA gene sequences and fluorescent in situ hybridization. The substrate had a major influence on the species of attached bacteria detected. Sequences retrieved from bran were dominated by clostridial cluster XIVa bacteria, including uncultured relatives of Clostridium hathewayi, Eubacterium rectale and Roseburia species. Bacteroides species were also detected. The most abundant sequences recovered from starch were related to the cultured species Ruminococcus bromii, Bifidobacterium adolescentis, Bifidobacterium breve and E. rectale. The most commonly recovered sequences from mucin were from Bifidobacterium bifidum and uncultured bacteria related to Ruminococcus lactaris. This study suggests that a specific subset of bacteria is likely to be the primary colonizers of particular insoluble colonic substrates. For a given substrate, however, the primary colonizing species may vary between host individuals.
Collapse
|
45
|
Dethlefsen L, Eckburg PB, Bik EM, Relman DA. Assembly of the human intestinal microbiota. Trends Ecol Evol 2006; 21:517-23. [PMID: 16820245 DOI: 10.1016/j.tree.2006.06.013] [Citation(s) in RCA: 311] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2005] [Revised: 05/18/2006] [Accepted: 06/15/2006] [Indexed: 12/12/2022]
Abstract
Complex microbial ecosystems occupy the skin, mucosa and alimentary tract of all mammals, including humans. Recent advances have highlighted the tremendous diversity of these microbial communities and their importance to host physiology, but questions remain about the ecological processes that establish and maintain the microbiota throughout life. The prevailing view, that the gastrointestinal microbiota of adult humans is a climax community comprised of the superior competitors for a stable set of niches, does not account for all of the experimental data. We argue here that the unique history of each community and intrinsic temporal dynamics also influence the structure of human intestinal communities.
Collapse
Affiliation(s)
- Les Dethlefsen
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | | | | | | |
Collapse
|