101
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Yin X, Yan Y, Kim EB, Lee B, Marco ML. Short communication: effect of milk and milk containing Lactobacillus casei on the intestinal microbiota of mice. J Dairy Sci 2014; 97:2049-55. [PMID: 24508432 DOI: 10.3168/jds.2013-7477] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 12/24/2013] [Indexed: 12/18/2022]
Abstract
BALB/c mice were fed milk or Lactobacillus casei BL23 in milk for 14d and fecal samples were collected at d 0, 4, and 7 as well as 1 and 8d after the last administration. According to high-throughput DNA sequencing of the 16S rRNA genes extracted from the fecal microbiota, the bacterial diversity in the fecal samples of all mice increased over time. After 14d of administration, the consumption of milk and milk containing L. casei BL23 resulted in distinct effects on the microbial composition in the intestine. Specifically, the proportions of bacteria in the Lactobacillaceae, Porphyromonadaceae, and Comamonadaceae were significantly higher in mice fed the L. casei BL23-milk culture compared with one or more of the other groups of mice. The relative amounts of Lachnospiraceae were higher and Streptococcaceae were lower in mice fed milk alone. The changes were not found at d 4 and 7 during milk and L. casei feeding and were no longer detected 8d after administration was stopped. This study shows that consumption of milk or probiotic L. casei-containing milk results in non-overlapping, taxa-specific effects on the bacteria in the distal murine intestine.
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Affiliation(s)
- Xiaochen Yin
- Department of Food Science & Technology, University of California, Davis 95616
| | - Yinzhuo Yan
- Department of Food Science & Technology, University of California, Davis 95616
| | - Eun Bae Kim
- Department of Food Science & Technology, University of California, Davis 95616
| | - Bokyung Lee
- Department of Food Science & Technology, University of California, Davis 95616
| | - Maria L Marco
- Department of Food Science & Technology, University of California, Davis 95616.
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102
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Eggerthella lenta bacteremia complicated by spondylodiscitis, psoas abscess, and meningitis. J Clin Microbiol 2014; 52:1278-80. [PMID: 24430458 DOI: 10.1128/jcm.03158-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Eggerthella lenta bacteremia is uncommon and generally associated with abdominal sepsis. The organism and its clinical significance have not been well characterized due to historical difficulties with identification. We report a case of severe infection in a paraplegic man complicated by psoas abscess, osteomyelitis, and meningitis and discuss treatment challenges.
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103
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Ni J, Yan Q, Yu Y, Zhang T. Factors influencing the grass carp gut microbiome and its effect on metabolism. FEMS Microbiol Ecol 2013; 87:704-14. [DOI: 10.1111/1574-6941.12256] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Revised: 11/12/2013] [Accepted: 11/14/2013] [Indexed: 12/11/2022] Open
Affiliation(s)
- Jiajia Ni
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- Guangdong Institute of Microbiology; Guangzhou China
- State Key Laboratory of Applied Microbiology; South China (The Ministry-Province Joint Development); Guangzhou China
| | - Qingyun Yan
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
| | - Yuhe Yu
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
| | - Tanglin Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
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104
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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.
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Affiliation(s)
- Xuan He
- Department of Nutrition and ‡Department of Food Science and Technology, University of California , Davis, California 95616, United States
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105
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Kemperman RA, Gross G, Mondot S, Possemiers S, Marzorati M, Van de Wiele T, Doré J, Vaughan EE. Impact of polyphenols from black tea and red wine/grape juice on a gut model microbiome. Food Res Int 2013. [DOI: 10.1016/j.foodres.2013.01.034] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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106
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Asano K, Yoshimura S, Nakane A. Alteration of intestinal microbiota in mice orally administered with salmon cartilage proteoglycan, a prophylactic agent. PLoS One 2013; 8:e75008. [PMID: 24040376 PMCID: PMC3767651 DOI: 10.1371/journal.pone.0075008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 08/08/2013] [Indexed: 12/20/2022] Open
Abstract
Proteoglycan (PG) extracted from salmon nasal cartilage has potential to be a prophylactic agent. Daily oral administration of the PG attenuates systemic inflammatory response in the experimental mouse models. In this study, we applied the culture-independent approach to investigate an alteration of intestinal microbiota composition in PG-administered mice. The results indicated that the population level of bacilli increased in the small and large intestine upon PG administration. On the other hand, the population level of clostridia decreased in the large intestine. The proportion of bacteria that are able to ferment saccharides and produce short-chain fatty acids increased in the small intestine and decreased in the large intestine. Importantly, population level of probiotic lactobacilli and bacteria exhibiting the immunomodulatory effect increased in the PG-administered mice. In addition, several disease-associated bacteria decreased upon PG administration. These results provided an understanding of the specific role of PG involved in host immune modulation and supported our hypothesis that daily oral administration of PG improves the overall balance in composition of the intestinal microbial community.
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Affiliation(s)
- Krisana Asano
- Department of Microbiology and Immunology, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori, Japan
| | - Sayuri Yoshimura
- Department of Microbiology and Immunology, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori, Japan
| | - Akio Nakane
- Department of Microbiology and Immunology, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori, Japan
- * E-mail:
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107
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Garcia TP, Müller S, Carroll RJ, Dunn TN, Thomas AP, Adams SH, Pillai SD, Walzem RL. Structured variable selection with q-values. Biostatistics 2013; 14:695-707. [PMID: 23580317 DOI: 10.1093/biostatistics/kxt012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
When some of the regressors can act on both the response and other explanatory variables, the already challenging problem of selecting variables when the number of covariates exceeds the sample size becomes more difficult. A motivating example is a metabolic study in mice that has diet groups and gut microbial percentages that may affect changes in multiple phenotypes related to body weight regulation. The data have more variables than observations and diet is known to act directly on the phenotypes as well as on some or potentially all of the microbial percentages. Interest lies in determining which gut microflora influence the phenotypes while accounting for the direct relationship between diet and the other variables A new methodology for variable selection in this context is presented that links the concept of q-values from multiple hypothesis testing to the recently developed weighted Lasso.
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Affiliation(s)
- Tanya P Garcia
- Department of Epidemiology and Biostatistics, Texas A&M Health Science Center, College Station, TX 77843-1266, USA
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108
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Xu B, Xu W, Yang F, Li J, Yang Y, Tang X, Mu Y, Zhou J, Huang Z. Metagenomic analysis of the pygmy loris fecal microbiome reveals unique functional capacity related to metabolism of aromatic compounds. PLoS One 2013; 8:e56565. [PMID: 23457582 PMCID: PMC3574064 DOI: 10.1371/journal.pone.0056565] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Accepted: 01/11/2013] [Indexed: 01/29/2023] Open
Abstract
The animal gastrointestinal tract contains a complex community of microbes, whose composition ultimately reflects the co-evolution of microorganisms with their animal host. An analysis of 78,619 pyrosequencing reads generated from pygmy loris fecal DNA extracts was performed to help better understand the microbial diversity and functional capacity of the pygmy loris gut microbiome. The taxonomic analysis of the metagenomic reads indicated that pygmy loris fecal microbiomes were dominated by Bacteroidetes and Proteobacteria phyla. The hierarchical clustering of several gastrointestinal metagenomes demonstrated the similarities of the microbial community structures of pygmy loris and mouse gut systems despite their differences in functional capacity. The comparative analysis of function classification revealed that the metagenome of the pygmy loris was characterized by an overrepresentation of those sequences involved in aromatic compound metabolism compared with humans and other animals. The key enzymes related to the benzoate degradation pathway were identified based on the Kyoto Encyclopedia of Genes and Genomes pathway assignment. These results would contribute to the limited body of primate metagenome studies and provide a framework for comparative metagenomic analysis between human and non-human primates, as well as a comparative understanding of the evolution of humans and their microbiome. However, future studies on the metagenome sequencing of pygmy loris and other prosimians regarding the effects of age, genetics, and environment on the composition and activity of the metagenomes are required.
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Affiliation(s)
- Bo Xu
- School of Life Science, Yunnan Normal University, Kunming, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, China
| | - Weijiang Xu
- School of Life Science, Yunnan Normal University, Kunming, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, China
| | - Fuya Yang
- School of Life Science, Yunnan Normal University, Kunming, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, China
| | - Junjun Li
- School of Life Science, Yunnan Normal University, Kunming, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, China
| | - Yunjuan Yang
- School of Life Science, Yunnan Normal University, Kunming, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, China
| | - Xianghua Tang
- School of Life Science, Yunnan Normal University, Kunming, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, China
| | - Yuelin Mu
- School of Life Science, Yunnan Normal University, Kunming, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, China
| | - Junpei Zhou
- School of Life Science, Yunnan Normal University, Kunming, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, China
| | - Zunxi Huang
- School of Life Science, Yunnan Normal University, Kunming, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, China
- * E-mail:
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109
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Gastrointestinal effects of resistant starch, soluble maize fibre and pullulan in healthy adults. Br J Nutr 2013; 110:1068-74. [DOI: 10.1017/s0007114513000019] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Fibre has been shown to exert a number of benefits on gastrointestinal (GI) health, yet its intake is low. Addition of novel fibres to food products may increase fibre intake and improve gut health. The objective of the present study was to evaluate the influence of three novel fibres on GI outcomes in healthy human subjects. A total of twenty healthy participants (ten men and ten women) with normal BMI (23 (sem 2) kg/m2) participated in the present randomised, double-blind, cross-over study with five treatment periods. Participants consumed a maltodextrin control or 20–25 g/d fibre from soluble maize fibre (SCF) or resistant starch (RS), alone or in combination with pullulan (SCF+P and RS+P). The treatment periods were 7 d with a 3-week washout between the periods. Stool samples were collected on day 7 of each period, and GI tolerance was assessed via a questionnaire on days 1 and 6. There were no treatment differences in stool weight or consistency. SCF significantly reduced stool pH and increased total SCFA production compared with RS and control. RS+P significantly increased the percentage of butyrate compared with all the other treatments. Overall, GI symptoms were minimal. SCF+P led to the highest GI score on day 1, while RS+P had the highest score on day 6. Both SCF treatments caused a significant shift in the gut microbial community. These functional fibres are generally well tolerated, have minimal effects on laxation and may lead to beneficial changes in SCFA production in healthy adults.
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110
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Inter-individual differences in response to dietary intervention: integrating omics platforms towards personalised dietary recommendations. Proc Nutr Soc 2013; 72:207-18. [PMID: 23388096 DOI: 10.1017/s0029665113000025] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Technologic advances now make it possible to collect large amounts of genetic, epigenetic, metabolomic and gut microbiome data. These data have the potential to transform approaches towards nutrition counselling by allowing us to recognise and embrace the metabolic, physiologic and genetic differences among individuals. The ultimate goal is to be able to integrate these multi-dimensional data so as to characterise the health status and disease risk of an individual and to provide personalised recommendations to maximise health. To this end, accurate and predictive systems-based measures of health are needed that incorporate molecular signatures of genes, transcripts, proteins, metabolites and microbes. Although we are making progress within each of these omics arenas, we have yet to integrate effectively multiple sources of biologic data so as to provide comprehensive phenotypic profiles. Observational studies have provided some insights into associative interactions between genetic or phenotypic variation and diet and their impact on health; however, very few human experimental studies have addressed these relationships. Dietary interventions that test prescribed diets in well-characterised study populations and that monitor system-wide responses (ideally using several omics platforms) are needed to make correlation-causation connections and to characterise phenotypes under controlled conditions. Given the growth in our knowledge, there is the potential to develop personalised dietary recommendations. However, developing these recommendations assumes that an improved understanding of the phenotypic complexities of individuals and their responses to the complexities of their diets will lead to a sustainable, effective approach to promote health and prevent disease - therein lies our challenge.
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111
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Xu X, Xu P, Ma C, Tang J, Zhang X. Gut microbiota, host health, and polysaccharides. Biotechnol Adv 2012; 31:318-37. [PMID: 23280014 DOI: 10.1016/j.biotechadv.2012.12.009] [Citation(s) in RCA: 169] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Revised: 12/20/2012] [Accepted: 12/21/2012] [Indexed: 02/07/2023]
Abstract
The intestinal microbiota is a complicated ecosystem that influences many aspects of host physiology (i.e. diet, disease development, drug metabolism, and regulation of the immune system). It also exhibits spatial patterning and temporal dynamics. In this review, the effects of internal and external (environmental) factors on intestinal microbiota are discussed. We describe the roles of the gut microbiota in maintaining intestinal and immune system homeostasis and the relationship between gut microbiota and diseases. In particular, the contributions of polysaccharides, as the most abundant diet components in intestinal microbiota and host health are presented. Finally, perspectives for research avenues relating to gut microbiota are also discussed.
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Affiliation(s)
- Xiaofei Xu
- College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, China
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112
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Eslami S, Barzgari Z, Saliani N, Saeedi N, Barzegari A. Annual fasting; the early calories restriction for cancer prevention. BIOIMPACTS : BI 2012; 2:213-215. [PMID: 23678462 PMCID: PMC3648937 DOI: 10.5681/bi.2012.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 12/05/2012] [Accepted: 12/06/2012] [Indexed: 06/02/2023]
Abstract
Essentially, people's diet and nutritional status has been changed substantially worldwide and several lines of evidence suggest that these changes are to the detriment of their health. Additionally, it has been well documented that unhealthy diet especially the fast foods, untraditional foods or bad-eating-habits influence the human gut microbiome. The gut microbiota shapes immune responses during human life and affects his/her metabolomic profiles. Furthermore, many studies highlight the molecular pathways that mediate host and symbiont interactions that regulate proper immune function and prevention of cancer in the body. Intriguingly, if cancer forms in a human body due to the weakness of immune system in detriment of microbiome, the removal of cancer stem cells can be carried out through early Calories Restriction with Annual Fasting (AF) before tumor development or progress. Besides, fasting can balance the gut microbiome for enhancement of immune system against cancer formation.
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Affiliation(s)
- Solat Eslami
- School of Advanced Medical Technologies, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | | | - Negar Saliani
- Department of Biology, Tehran University, Tehran, Iran
| | - Nazli Saeedi
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Science, Tabriz, Iran
| | - Abolfazl Barzegari
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Science, Tabriz, Iran
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113
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Sun X, Waghorn G, Hoskin S, Harrison S, Muetzel S, Pacheco D. Methane emissions from sheep fed fresh brassicas (Brassica spp.) compared to perennial ryegrass (Lolium perenne). Anim Feed Sci Technol 2012. [DOI: 10.1016/j.anifeedsci.2012.07.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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114
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Abstract
PURPOSE OF REVIEW Humans harbor microbial communities throughout the gastrointestinal tract that both respond to and modify orally ingested macronutrients, bioactive compounds, and xenobiotics; for example, the metabolism of polyphenols, heterocyclic amines, and phosphatidylcholine. However, the composition and physiological impact of our diet is also linked to the methods of food production, preparation, and consumption, which are altered by environmental and food-borne microbial communities. Metagenomic analyses spanning these various steps in human nutrition will be critical for a more comprehensive view. RECENT FINDINGS Studies in humans and animal models have highlighted the key role that diet plays in shaping gut microbial ecology, and how the trillions of microbes in the gut (microbiota) enable the digestion of substrates inaccessible to our own human enzymes. These transformations have been implicated in a variety of diseases and disorders, ranging from obesity, inflammatory bowel disease, heart disease, to cancer. SUMMARY In order to move towards personalized nutrition and medicine, it is important to take into account both our host and microbial genomes. The resulting metagenomic view of human nutrition, ranging from the initial biotransformations of food to digestion and the end result on human physiology, could have wide-ranging implications for food science, human evolutionary biology, and microbial ecology.
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Affiliation(s)
- Rachel J Dutton
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, USA
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115
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Staudacher HM, Lomer MCE, Anderson JL, Barrett JS, Muir JG, Irving PM, Whelan K. Fermentable carbohydrate restriction reduces luminal bifidobacteria and gastrointestinal symptoms in patients with irritable bowel syndrome. J Nutr 2012; 142:1510-8. [PMID: 22739368 DOI: 10.3945/jn.112.159285] [Citation(s) in RCA: 355] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Preliminary studies indicate that dietary restriction of fermentable short-chain carbohydrates improves symptoms in irritable bowel syndrome (IBS). Prebiotic fructo-oligosaccharides and galacto-oligosaccharides stimulate colonic bifidobacteria. However, the effect of restricting fermentable short-chain carbohydrates on the gastrointestinal (GI) microbiota has never been examined. This randomized controlled trial aimed to investigate the effects of fermentable carbohydrate restriction on luminal microbiota, SCFA, and GI symptoms in patients with IBS. Patients with IBS were randomized to the intervention diet or habitual diet for 4 wk. The incidence and severity of symptoms and stool output were recorded for 7 d at baseline and follow-up. A stool sample was collected and analyzed for bacterial groups using fluorescent in situ hybridization. Of 41 patients randomized, 6 were withdrawn. At follow-up, there was lower intake of total short-chain fermentable carbohydrates in the intervention group compared with controls (P = 0.001). The total luminal bacteria at follow-up did not differ between groups; however, there were lower concentrations (P < 0.001) and proportions (P < 0.001) of bifidobacteria in the intervention group compared with controls when adjusted for baseline. In the intention-to-treat analysis, more patients in the intervention group reported adequate control of symptoms (13/19, 68%) compared with controls (5/22, 23%; P = 0.005). This randomized controlled trial demonstrated a reduction in concentration and proportion of luminal bifidobacteria after 4 wk of fermentable carbohydrate restriction. Although the intervention was effective in managing IBS symptoms, the implications of its effect on the GI microbiota are still to be determined.
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Affiliation(s)
- Heidi M Staudacher
- King's College London, School of Medicine, Diabetes and Nutritional Sciences Division, London, UK
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116
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Lagier JC, Armougom F, Mishra AK, Nguyen TT, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Alistipes timonensis sp. nov. Stand Genomic Sci 2012. [DOI: 10.4056/sigs.2685917] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Jean-Christophe Lagier
- 1Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR, Aix-Marseille Université, Marseille, France
| | - Fabrice Armougom
- 1Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR, Aix-Marseille Université, Marseille, France
| | - Ajay Kumar Mishra
- 1Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR, Aix-Marseille Université, Marseille, France
| | - Thi-Tien Nguyen
- 1Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR, Aix-Marseille Université, Marseille, France
| | - Didier Raoult
- 1Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR, Aix-Marseille Université, Marseille, France
| | - Pierre-Edouard Fournier
- 1Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR, Aix-Marseille Université, Marseille, France
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117
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Lagier JC, Armougom F, Mishra AK, Nguyen TT, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Alistipes timonensis sp. nov. Stand Genomic Sci 2012; 6:315-24. [PMID: 23408657 PMCID: PMC3558960 DOI: 10.4056/sigs.2685971] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Alistipes timonensis strain JC136T sp. nov. is the type strain of A. timonensis sp. nov., a new species within the genus Alistipes. This strain, whose genome is described here, was isolated from the fecal flora of a healthy patient. A. timonensis is an obligate anaerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,497,779 bp long genome (one chromosome but no plasmid) contains 2,742 protein-coding and 50 RNA genes, including three rRNA genes.
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Affiliation(s)
- Jean-Christophe Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR, Aix-Marseille Université, Marseille, France
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118
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Rosendale D, Butts C, de Guzman E, Maddox I, Martell S, McIntyre L, Skinner M, Smith H, Ansell J. The contribution of dietary broccoli sprouts towards the microbial metabolite profile in the hind gut of mice. Int J Food Sci Technol 2012. [DOI: 10.1111/j.1365-2621.2012.02947.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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119
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Draft genome sequence of Gluconobacter morbifer G707T, a pathogenic gut bacterium isolated from Drosophila melanogaster intestine. J Bacteriol 2012; 194:1245. [PMID: 22328748 DOI: 10.1128/jb.06670-11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gluconobacter morbifer G707(T), a minor member of gut microbiota, was isolated from fruit fly (Drosophila melanogaster). Here, the draft genome sequence of Gluconobacter morbifer G707(T) is reported.
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120
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Day L, Gomez J, Øiseth SK, Gidley MJ, Williams BA. Faster fermentation of cooked carrot cell clusters compared to cell wall fragments in vitro by porcine feces. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:3282-3290. [PMID: 22385330 DOI: 10.1021/jf204974s] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Plant cell walls are the major structural component of fruits and vegetables, which break down to cell wall particles during ingestion (oral mastication) or food processing. The major health-promoting effect of cell walls occurs when they reach the colon and are fermented by the gut microbiota. In this study, the fermentation kinetics of carrot cell wall particle dispersions with different particle size and microstructure were investigated in vitro using porcine feces. The cumulative gas production and short-chain fatty acids (SCFAs) produced were measured at time intervals up to 48 h. The results show that larger cell clusters with an average particle size (d(0.5)) of 298 and 137 μm were more rapidly fermented and produced more SCFAs and gas than smaller single cells (75 μm) or cell fragments (50 μm), particularly between 8 and 20 h. Confocal microscopy suggests that the junctions between cells provides an environment that promotes bacterial growth, outweighing the greater specific surface area of smaller particles as a driver for more rapid fermentation. The study demonstrates that it may be possible, by controlling the size of cell wall particles, to design plant-based foods for fiber delivery and promotion of colon fermentation to maximize the potential for human health.
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Affiliation(s)
- Li Day
- CSIRO Food and Nutritional Sciences, 671 Sneydes Road, Werribee, Victoria 3030, Australia.
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Navarro SL, Li F, Lampe JW. Mechanisms of action of isothiocyanates in cancer chemoprevention: an update. Food Funct 2011; 2:579-87. [PMID: 21935537 PMCID: PMC3204939 DOI: 10.1039/c1fo10114e] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Isothiocyanates (ITC), derived from glucosinolates, are thought to be responsible for the chemoprotective actions conferred by higher cruciferous vegetable intake. Evidence suggests that isothiocyanates exert their effects through a variety of distinct but interconnected signaling pathways important for inhibiting carcinogenesis, including those involved in detoxification, inflammation, apoptosis, and cell cycle and epigenetic regulation, among others. This article provides an update on the latest research on isothiocyanates and these mechanisms, and points out remaining gaps in our understanding of these events. Given the variety of ITC produced from glucosinolates, and the diverse pathways on which these compounds act, a systems biology approach, in vivo, may help to better characterize their integrated role in cancer prevention. In addition, the effects of dose, duration of exposure, and specificity of different ITC should be considered.
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Affiliation(s)
- Sandi L. Navarro
- Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA, 98109
- Interdisciplinary Graduate Program in Nutritional Sciences, Department of Epidemiology, University of Washington, Seattle, WA 98195
| | - Fei Li
- Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA, 98109
| | - Johanna W. Lampe
- Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA, 98109
- Interdisciplinary Graduate Program in Nutritional Sciences, Department of Epidemiology, University of Washington, Seattle, WA 98195
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122
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Molecular fingerprints of the human fecal microbiota from 9 to 18 months old and the effect of fish oil supplementation. J Pediatr Gastroenterol Nutr 2011; 53:303-9. [PMID: 21865979 DOI: 10.1097/mpg.0b013e31821d298f] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVES The aim of this study was to monitor changes in the fecal microbiota from 9 to 18 months and to investigate the effect of increasing dietary n-3 polyunsaturated fatty acids on the fecal microbiota. PATIENTS AND METHODS In a double-blind controlled trial with random allocation to daily supplementation with 5 mL of fish oil (FO) or sunflower oil (SO) from 9 to 18 months of age, stool samples were collected from 132 healthy Danish infants. Molecular fingerprints of the bacterial DNA were obtained by terminal restriction fragment length polymorphism (T-RFLP). RESULTS The T-RFLP profiles indicated that a few T-RFs became dominant with age (bp100 and 102, both presumed to be Bacteroidetes) concomitantly with an overall increase in the microbial diversity (P = 0.04). Breast-feeding influenced both the T-RFLP profiles at 9 months and the changes from 9 to 18 months, and breast-feeding cessation during the trial modified the response to the dietary oils. In the FO group, the increase in bp102 was significantly reduced among children weaned before compared with those weaned during the trial (P = 0.027), whereas the increase in bp100 was reduced in the preweaned children of the SO group relative to those weaned during the trial (P = 0.004). This was supported by intervention group differences in the changes in bp102 and bp100 among the earlier weaned children (P = 0.06 and P = 0.09, respectively). CONCLUSIONS Cessation of breast-feeding played a dominant role relative to developmental changes in the fecal microbiota from 9 to 18 months. FO compared with SO supplementation affected changes in large bacterial groups, but only among children who had stopped breast-feeding before 9 months of age.
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123
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Traka MH, Mithen RF. Plant science and human nutrition: challenges in assessing health-promoting properties of phytochemicals. THE PLANT CELL 2011; 23:2483-97. [PMID: 21803940 PMCID: PMC3226206 DOI: 10.1105/tpc.111.087916] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 07/15/2011] [Accepted: 07/15/2011] [Indexed: 05/20/2023]
Abstract
The rise in noncommunicable chronic diseases associated with changing diet and lifestyles throughout the world is a major challenge for society. It is possible that certain dietary components within plants have roles both in reducing the incidence and progression of these diseases. We critically review the types of evidence used to support the health promoting activities of certain phytochemicals and plant-based foods and summarize the major contributions but also the limitations of epidemiological and observational studies and research with the use of cell and animal models. We stress the need for human intervention studies to provide high-quality evidence for health benefits of dietary components derived from plants.
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Abstract
Glucosinolates, phytochemicals found in cruciferous vegetables, are metabolised to bioactive isothiocyanates (ITC) by certain bacteria in the human gut. Substantial individual variation in urinary ITC excretion has been observed in previous cruciferous vegetable-feeding studies. We hypothesised that individual differences in gut microbial community contribute to the observed variation in glucosinolate metabolism, i.e. gut microbiota composition between high- and low-ITC excreters differs. We recruited twenty-three healthy individuals and fed them a standardised meal containing 200 g of cooked broccoli. After the meal, 24 h urinary ITC excretion was measured. Study participants with the highest (n 5) and lowest (n 5) ITC excretion provided faecal samples for ex vivo bacterial cultivation with 50 μm-glucoraphanin, the major glucosinolate found in broccoli. When grown ex vivo, faecal bacteria from the selected high-ITC excreters were able to degrade more glucoraphanin than those from the low-ITC excreters (P = 0·05). However, bacterial fingerprints of faecal and ex vivo culture microbiota revealed no statistically significant differences between the high- and low-ITC excreters in terminal restriction fragment length polymorphism analysis of the bacterial 16S ribosomal RNA gene. In conclusion, glucosinolate degradation by faecal bacteria ex vivo may be associated with in vivo bacterial glucosinolate metabolism capacity, but no direct link to specific bacterial species could be established, possibly due to the complexity and functional redundancy of the gut microbiota.
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125
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Zhou X, Brotman RM, Gajer P, Abdo Z, Schüette U, Ma S, Ravel J, Forney LJ. Recent advances in understanding the microbiology of the female reproductive tract and the causes of premature birth. Infect Dis Obstet Gynecol 2010; 2010:737425. [PMID: 21197076 PMCID: PMC3004384 DOI: 10.1155/2010/737425] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Accepted: 10/25/2010] [Indexed: 02/07/2023] Open
Abstract
Data derived from molecular microbiological investigations of the human vagina have led to the discovery of resident bacterial communities that exhibit marked differences in terms of species composition. All undergo dynamic changes that are likely due to intrinsic host and behavioral factors. Similar types of bacteria have been found in both amniotic fluid and the vagina, suggesting a potential route of colonization. Given that not all of the species involved in intrauterine infections are readily cultivated, it is important that culture-independent methods of analysis must be used to understand the etiology of these infections. Further research is needed to establish whether an ascending pathway from the vagina to the amniotic cavity enables the development of intrauterine infections.
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Affiliation(s)
- Xia Zhou
- Initiative for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID 83844-3051, USA
- Department of Biological Sciences, Life Sciences South, Rm. 441A, University of Idaho, Moscow, ID 83844-3150, USA
| | - Rebecca M. Brotman
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201-1559, USA
| | - Pawel Gajer
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201-1559, USA
| | - Zaid Abdo
- Initiative for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID 83844-3051, USA
- Department of Mathematics, University of Idaho, Moscow, ID 83844-3051, USA
- Department of Statistics, University of Idaho, Moscow, ID 83844-3051, USA
| | - Ursel Schüette
- Initiative for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID 83844-3051, USA
- Department of Biological Sciences, Life Sciences South, Rm. 441A, University of Idaho, Moscow, ID 83844-3150, USA
| | - Sam Ma
- Initiative for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID 83844-3051, USA
- Department of Biological Sciences, Life Sciences South, Rm. 441A, University of Idaho, Moscow, ID 83844-3150, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201-1559, USA
| | - Larry J. Forney
- Initiative for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID 83844-3051, USA
- Department of Biological Sciences, Life Sciences South, Rm. 441A, University of Idaho, Moscow, ID 83844-3150, USA
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Lai RH, Miller MJ, Jeffery E. Glucoraphanin hydrolysis by microbiota in the rat cecum results in sulforaphane absorption. Food Funct 2010; 1:161-6. [PMID: 21776467 DOI: 10.1039/c0fo00110d] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the absence of the plant enzyme myrosinase, such as in cooked broccoli, glucoraphanin is considered to be hydrolyzed by bacteria in the lower gut to produce the bioactive isothiocyanate sulforaphane. Simulated digestion using US Pharmacopeia methods caused no loss of glucoraphanin, confirming that glucoraphanin is not destroyed by digestive enzymes during passage through the digestive tract and is able to reach the rat cecum intact. Introduction of glucoraphanin (150 μmol/kg BW) directly into the cecum resulted in appearance of isothiocyanates in the mesenteric plasma by 120 min. In contrast, introduction of sulforaphane (150 μmol/kg BW) directly into the cecum resulted in the appearance of isothiocyanates in the mesenteric plasma within 15 min. Plasma levels remained constant for over an hour. Anaerobic incubation ex vivo of cecal microbiota from male F344 rats with glucoraphanin resulted in very low levels of the hydrolytic metabolite erucin nitrile, showing that hydrolysis of glucosinolates is carried out by cecal microbiota, but metabolism ex vivo by microbiota did not reflect not reflect metabolism in situ. These data are the first to report direct evidence of hydrolysis of glucoraphanin to sulforaphane in the cecum of rats and to show that sulforaphane is able to cross the cecal enterocyte for systemic absorption.
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Affiliation(s)
- Ren-Hau Lai
- Division of Nutritional Sciences, University of Illinois, 905 S Goodwin Ave, Urbana, IL 61801, USA
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127
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Swanson KS, Dowd SE, Suchodolski JS, Middelbos IS, Vester BM, Barry KA, Nelson KE, Torralba M, Henrissat B, Coutinho PM, Cann IKO, White BA, Fahey GC. Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice. ISME JOURNAL 2010; 5:639-49. [PMID: 20962874 PMCID: PMC3105739 DOI: 10.1038/ismej.2010.162] [Citation(s) in RCA: 237] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This study is the first to use a metagenomics approach to characterize the phylogeny and functional capacity of the canine gastrointestinal microbiome. Six healthy adult dogs were used in a crossover design and fed a low-fiber control diet (K9C) or one containing 7.5% beet pulp (K9BP). Pooled fecal DNA samples from each treatment were subjected to 454 pyrosequencing, generating 503 280 (K9C) and 505 061 (K9BP) sequences. Dominant bacterial phyla included the Bacteroidetes/Chlorobi group and Firmicutes, both of which comprised ∼35% of all sequences, followed by Proteobacteria (13–15%) and Fusobacteria (7–8%). K9C had a greater percentage of Bacteroidetes, Fusobacteria and Proteobacteria, whereas K9BP had greater proportions of the Bacteroidetes/Chlorobi group and Firmicutes. Archaea were not altered by diet and represented ∼1% of all sequences. All archaea were members of Crenarchaeota and Euryarchaeota, with methanogens being the most abundant and diverse. Three fungi phylotypes were present in K9C, but none in K9BP. Less than 0.4% of sequences were of viral origin, with >99% of them associated with bacteriophages. Primary functional categories were not significantly affected by diet and were associated with carbohydrates; protein metabolism; DNA metabolism; cofactors, vitamins, prosthetic groups and pigments; amino acids and derivatives; cell wall and capsule; and virulence. Hierarchical clustering of several gastrointestinal metagenomes demonstrated phylogenetic and metabolic similarity between dogs, humans and mice. More research is required to provide deeper coverage of the canine microbiome, evaluate effects of age, genetics or environment on its composition and activity, and identify its role in gastrointestinal disease.
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Affiliation(s)
- Kelly S Swanson
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA
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Rogers GB, Carroll MP, Hoffman LR, Walker AW, Fine DA, Bruce KD. Comparing the microbiota of the cystic fibrosis lung and human gut. Gut Microbes 2010; 1:85-93. [PMID: 21326915 PMCID: PMC3023585 DOI: 10.4161/gmic.1.2.11350] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Revised: 01/25/2010] [Accepted: 01/29/2010] [Indexed: 02/08/2023] Open
Affiliation(s)
- Geraint B Rogers
- King's College London; Molecular Microbiology Research Laboratory; Pharmaceutical Science Division; London, UK
| | - Mary P Carroll
- Cystic Fibrosis Unit Southampton University Hospitals NHS Trust; Southampton, UK
| | | | - Alan W Walker
- Wellcome Trust Sanger Institute; Hinxton, Cambridge UK
| | - David A Fine
- Gastroenterology; Southampton University Hospitals NHS Trust; Southampton, UK
| | - Kenneth D Bruce
- King's College London; Molecular Microbiology Research Laboratory; Pharmaceutical Science Division; London, UK
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