DOCSLIB.ORG

Nondigestible Carbohydrates, Butyrate, and Butyrate-Producing Bacteria

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Nondigestible Carbohydrates, Butyrate, and Butyrate-Producing Bacteria Critical Reviews in Food Science and Nutrition ISSN: 1040-8398 (Print) 1549-7852 (Online) Journal homepage: https://www.tandfonline.com/loi/bfsn20 Nondigestible carbohydrates, butyrate, and butyrate-producing bacteria Xiaodan Fu, Zhemin Liu, Changliang Zhu, Haijin Mou & Qing Kong To cite this article: Xiaodan Fu, Zhemin Liu, Changliang Zhu, Haijin Mou & Qing Kong (2018): Nondigestible carbohydrates, butyrate, and butyrate-producing bacteria, Critical Reviews in Food Science and Nutrition, DOI: 10.1080/10408398.2018.1542587 To link to this article: https://doi.org/10.1080/10408398.2018.1542587 Published online: 22 Dec 2018. Submit your article to this journal Article views: 112 View Crossmark data Full Terms & Conditions of access and use can be found at https://www.tandfonline.com/action/journalInformation?journalCode=bfsn20 CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION https://doi.org/10.1080/10408398.2018.1542587 REVIEW Nondigestible carbohydrates, butyrate, and butyrate-producing bacteria Xiaodan Fu, Zhemin Liu, Changliang Zhu, Haijin Mou, and Qing Kong College of Food Science and Engineering, Ocean University of China, Qingdao, China ABSTRACT KEYWORDS Nondigestible carbohydrates (NDCs) are fermentation substrates in the colon after escaping diges- Nondigestible carbohy- tion in the upper gastrointestinal tract. Among NDCs, resistant starch is not hydrolyzed by pancre- drates; oligosaccharides; atic amylases but can be degraded by enzymes produced by large intestinal bacteria, including short-chain fatty acids; butyrate; butyrate- clostridia, bacteroides, and bifidobacteria. Nonstarch polysaccharides, such as pectin, guar gum, producing bacteria alginate, arabinoxylan, and inulin fructans, and nondigestible oligosaccharides and their deriva- tives, 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 func- tions 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. Introduction shown to play an important role in modulating immune and inflammatory responses and intestinal barrier function Studies on nondigestible carbohydrates (NDCs), including and in preventing colon cancers (Hamer et al. 2008; Elamin undigested plant polysaccharides, resistant starch (RS), and et al. 2013). Furthermore, recent studies have shown that nondigestible oligosaccharides (NDOs), have attracted atten- NDCs consumption and dietary butyrate supplementation tion owing to the functions of these materials as dietary have beneficial effects on health by decreasing adiposity and fibers (DFs) (Mussatto and Mancilha 2007; Smith and improving insulin sensitivity (McNabney and Henagan 2017; Tucker 2011; Holscher 2017). Human enzymes are capable Henagan et al. 2015). of degrading only a few glycosidic linkages present in carbo- In recent years, specific gut microbiota has attracted hydrates; however, intestinal bacteria possess many enzymes, attention owing to their important roles in gut metabolism including glycoside hydrolases, polysaccharide lyases, glyco- and homeostasis. In particularly, butyrogenic bacteria from syltransferases, and carbohydrate esterases, that are necessary within the Firmicutes/Clostridium clusters IV and XIVa have for carbohydrate utilization (Englyst, Hay, and Macfarlane been taken as probiotics to increase colonic butyrate levels 1987; Lombard et al. 2014). Thus, NDCs can escape diges- and optimize gut health (Scott et al. 2014; Hossain, Begum, tion in the host gastrointestinal tract to be metabolized by and Kim 2015). Various strategies are available to enhance the microbiota in the cecum and colon (Ning et al. 2017). butyrate levels in the distal intestine. Supplementation with The metabolism of NDCs generate a variety of products, NDCs, such as RS (Brouns, Kettlitz, and Arrigoni 2002), including short-chain fatty acids (SCFAs; e.g., acetate, propi- psyllium fiber (Marteau et al. 1994), and guar gum (Pylkas, onate, and butyrate), gases (e.g., H2,H2S, CO2, and CH4), Juneja, and Slavin 2005), is another widely recognized and organic acids (e.g., lactate, succinate, and pyruvate), approach. Butyrate production of NDCs can be influenced which affect the host health to different extents (Macfarlane by many factors, such as the solubility, the distribution of and Macfarlane 2012; Koh et al. 2016). chain lengths, branching and substituents, the monomeric SCFAs, primarily acetate, propionate, and butyrate, have carbohydrate composition, and linkage type between mono- been estimated to provide approximately 60–70% of the mers (Karppinen et al. 2000; Henningsson, Bjorck,€ and energy requirements of colonic epithelial cells (Brahe, Nyman 2002; Nilsson and Nyman 2005). Additionally, Astrup, and Larsen 2013). Specifically, the four-carbon cross-feeding interactions between bacteria also affect SCFA butyrate is the major energy source for colonocytes, colonic fermentation through modulating microbial mutual- directly affecting the growth and differentiation of these cells istic symbiosis and competitive fitness (Morrison and (Jacobi and Odle 2012; Chen et al. 2015). Butyrate has been Preston 2016). However, the current understanding on the CONTACT Haijin Mou [email protected]; Qing Kong [email protected] Ocean University of China, College of Food Science and Engineering, No. 5 Yushan Road, Qingdao 266003, Shandong, China. Color versions of one or more of the figures in the article can be found online at www.tandfonline.com/bfsn. ß 2018 Taylor & Francis Group, LLC 2 X. FU ET AL. composition and metabolism of intestinal microbiota is still individual variations in microbiota composition (Karppinen insufficient, which limits the application of this approach. et al. 2000; Henningsson, Bjorck,€ and Nyman 2002;Nilsson In this review, we summarize recent studies on NDCs and Nyman 2005; Louis et al. 2010). Moreover, the gut with butyrogenic effects, factors affecting butyrate produc- bacteria differ in their possession of degradative enzymes and tion, and physiological effects and mechanism of butyrate. transport systems, which likely determines the substrate pref- Based on our analysis, the strategies of combining different erence and competitive ability of a given bacteria, and conse- NDCs and probiotic bacterial strains related with butyrate- quently the butyrate-producing ability (Flint 2004;vander production can be potentially meaningful to achieve direc- Meulen et al. 2006). tional accumulation of colonic butyrate. Previously described butyrate-producing bacteria in the human gastrointestinal intestinal tract are commonly distrib- uted in the phylum Firmicutes and the order Clostridiales Butyrate production and physiological effects (Table. 1). The majority of these producers belong to four fam- Butyrate production from NDCs ilies: Clostridiaceae, Eubacteriaceae, Lachnospiraceae, and Ruminococcaceae; however, not all the members within these The human large intestine contains a very dense microbial families are butyrogenic (Duncan et al. 2002;Louisetal.2004; (>1011 bacteria per gram) community composed largely of a Louis and Flint 2009;Vital,Howe,andTiedje2014). Members metabolically active microbiota (Flint et al. 2007). This com- within other families such as Veillonellaceae (e.g., Megasphaera munity plays an important role in health and largely elsdenii) and Thermoanaerobacterales Family III (e.g., depends on dietary carbohydrate as an energy source. Most Caldocellum saccharolyticum) have also been identified as of these carbohydrates cannot be degraded by the host and butyrate producers (Louis et al. 2004; Tsukahara et al. 2002). are therefore broken down by the gut microbiota owing to Most butyrate producers in the order Clostridiales are widely their more excellent degradative enzymes and metabolic distributed across several clusters including clusters IV, XIVa, capabilities than their hosts (Flint et al. 2008; Kurokawa XVI, and I. Among them, two of the most important groups, et al. 2007). Most of the dietary carbohydrates that reach the F. prausnitzii (clostridial cluster IV) and Eubacterium rectale large intestine are generally insoluble fragments of plant (clostridial cluster XIVa), have been studied extensively because fiber, which largely consists of plant cell-wall polysaccharides they typically constitute up to 12 À 14% of the total gut micro- and starch particles, as well as oligosaccharides and storage polysaccharides (Flint et al. 2008). However, only a few gut biota in fecal samples of healthy adults based on 16S rRNA bacteria are available to degrade the insoluble substrates. gene sequencing (Walker et al., 2014). Moreover, other typical Specialized primary degraders, typically cellulolytic bacteria, butyrogenic species are also widely distributed across cluster are able to release a wider range of solubilized products (e.g. XIVa (e.g., Roseburia spp., Anaerostipes spp., Clostridium spp., polysaccharides and oligosaccharides)
Load more

Recommended publications
  • Supplementary Materials
    Supplementary Materials Figure S1. Differentially abundant spots between the mid-log phase cells grown on xylan or xylose. Red and blue circles denote spots with increased and decreased abundance respectively in the xylan growth condition. The identities of the circled spots are summarized in Table 3. Figure S2. Differentially abundant spots between the stationary phase cells grown on xylan or xylose. Red and blue circles denote spots with increased and decreased abundance respectively in the xylan growth condition. The identities of the circled spots are summarized in Table 4. S2 Table S1. Summary of the non-polysaccharide degrading proteins identified in the B. proteoclasticus cytosol by 2DE/MALDI-TOF. Protein Locus Location Score pI kDa Pep. Cov. Amino Acid Biosynthesis Acetylornithine aminotransferase, ArgD Bpr_I1809 C 1.7 × 10−4 5.1 43.9 11 34% Aspartate/tyrosine/aromatic aminotransferase Bpr_I2631 C 3.0 × 10−14 4.7 43.8 15 46% Aspartate-semialdehyde dehydrogenase, Asd Bpr_I1664 C 7.6 × 10−18 5.5 40.1 17 50% Branched-chain amino acid aminotransferase, IlvE Bpr_I1650 C 2.4 × 10−12 5.2 39.2 13 32% Cysteine synthase, CysK Bpr_I1089 C 1.9 × 10−13 5.0 32.3 18 72% Diaminopimelate dehydrogenase Bpr_I0298 C 9.6 × 10−16 5.6 35.8 16 49% Dihydrodipicolinate reductase, DapB Bpr_I2453 C 2.7 × 10−6 4.9 27.0 9 46% Glu/Leu/Phe/Val dehydrogenase Bpr_I2129 C 1.2 × 10−30 5.4 48.6 31 64% Imidazole glycerol phosphate synthase Bpr_I1240 C 8.0 × 10−3 4.7 22.5 8 44% glutamine amidotransferase subunit Ketol-acid reductoisomerase, IlvC Bpr_I1657 C 3.8 × 10−16
    [Show full text]
  • Detoxification of Lignocellulose-Derived Microbial Inhibitory Compounds by Clostridium Beijerinckii NCIMB 8052 During Acetone-Butanol-Ethanol Fermentation
    Detoxification of Lignocellulose-derived Microbial Inhibitory Compounds by Clostridium beijerinckii NCIMB 8052 during Acetone-Butanol-Ethanol Fermentation DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Yan Zhang Graduate Program in Animal Sciences The Ohio State University 2013 Dissertation Committee: Thaddeus C. Ezeji, Advisor Steven C. Loerch Sandra G. Velleman Zhongtang Yu Venkat Gopalan Copyrighted by Yan Zhang 2013 Abstract Pretreatment and hydrolysis of lignocellulosic biomass to fermentable sugars generate a complex mixture of microbial inhibitors such as furan aldehydes (e.g., furfural), which at sublethal concentration in the fermentation medium can be tolerated or detoxified by acetone butanol ethanol (ABE)-producing Clostridium beijerinckii NCIMB 8052. The response of C. beijerinckii to furfural at the molecular level, however, has not been directly studied. Therefore, this study was to elucidate mechanism employed by C. beijerinckii to detoxify lignocellulose-derived microbial inhibitors and use this information to develop inhibitor-tolerant C. beijerinckii. Towards the long-term goal of developing inhibitor-tolerant Clostridium strains, the first objective was to evaluate ABE fermentation by C. beijerinckii using different proportions of Miscanthus giganteus hydrolysates as carbon source. Compared to the growth of C. beijerinckii in control medium, C. beijerinckii experienced different degrees of inhibition. The degree of inhibition was dose-dependent, and C. beijerinckii did not grow in P2 medium with greater than 25% (v/v) Miscanthus giganteus hydrolysates. To improve tolerance of C. beijerinckii to inhibitors, supplementation of P2 medium with undiluted (100%) Miscanthus giganteus hydrolysates with 4 g/L CaCO3 resulted in successful growth of and ABE production by C.
    [Show full text]
  • Gut Microbiota Differs in Composition and Functionality Between Children
    Diabetes Care Volume 41, November 2018 2385 Gut Microbiota Differs in Isabel Leiva-Gea,1 Lidia Sanchez-Alcoholado,´ 2 Composition and Functionality Beatriz Mart´ın-Tejedor,1 Daniel Castellano-Castillo,2,3 Between Children With Type 1 Isabel Moreno-Indias,2,3 Antonio Urda-Cardona,1 Diabetes and MODY2 and Healthy Francisco J. Tinahones,2,3 Jose´ Carlos Fernandez-Garc´ ´ıa,2,3 and Control Subjects: A Case-Control Mar´ıa Isabel Queipo-Ortuno~ 2,3 Study Diabetes Care 2018;41:2385–2395 | https://doi.org/10.2337/dc18-0253 OBJECTIVE Type 1 diabetes is associated with compositional differences in gut microbiota. To date, no microbiome studies have been performed in maturity-onset diabetes of the young 2 (MODY2), a monogenic cause of diabetes. Gut microbiota of type 1 diabetes, MODY2, and healthy control subjects was compared. PATHOPHYSIOLOGY/COMPLICATIONS RESEARCH DESIGN AND METHODS This was a case-control study in 15 children with type 1 diabetes, 15 children with MODY2, and 13 healthy children. Metabolic control and potential factors mod- ifying gut microbiota were controlled. Microbiome composition was determined by 16S rRNA pyrosequencing. 1Pediatric Endocrinology, Hospital Materno- Infantil, Malaga,´ Spain RESULTS 2Clinical Management Unit of Endocrinology and Compared with healthy control subjects, type 1 diabetes was associated with a Nutrition, Laboratory of the Biomedical Research significantly lower microbiota diversity, a significantly higher relative abundance of Institute of Malaga,´ Virgen de la Victoria Uni- Bacteroides Ruminococcus Veillonella Blautia Streptococcus versityHospital,Universidad de Malaga,M´ alaga,´ , , , , and genera, and a Spain lower relative abundance of Bifidobacterium, Roseburia, Faecalibacterium, and 3Centro de Investigacion´ BiomedicaenRed(CIBER)´ Lachnospira.
    [Show full text]
  • The Microbiota-Produced N-Formyl Peptide Fmlf Promotes Obesity-Induced Glucose
    Page 1 of 230 Diabetes Title: The microbiota-produced N-formyl peptide fMLF promotes obesity-induced glucose intolerance Joshua Wollam1, Matthew Riopel1, Yong-Jiang Xu1,2, Andrew M. F. Johnson1, Jachelle M. Ofrecio1, Wei Ying1, Dalila El Ouarrat1, Luisa S. Chan3, Andrew W. Han3, Nadir A. Mahmood3, Caitlin N. Ryan3, Yun Sok Lee1, Jeramie D. Watrous1,2, Mahendra D. Chordia4, Dongfeng Pan4, Mohit Jain1,2, Jerrold M. Olefsky1 * Affiliations: 1 Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, California, USA. 2 Department of Pharmacology, University of California, San Diego, La Jolla, California, USA. 3 Second Genome, Inc., South San Francisco, California, USA. 4 Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA. * Correspondence to: 858-534-2230, [email protected] Word Count: 4749 Figures: 6 Supplemental Figures: 11 Supplemental Tables: 5 1 Diabetes Publish Ahead of Print, published online April 22, 2019 Diabetes Page 2 of 230 ABSTRACT The composition of the gastrointestinal (GI) microbiota and associated metabolites changes dramatically with diet and the development of obesity. Although many correlations have been described, specific mechanistic links between these changes and glucose homeostasis remain to be defined. Here we show that blood and intestinal levels of the microbiota-produced N-formyl peptide, formyl-methionyl-leucyl-phenylalanine (fMLF), are elevated in high fat diet (HFD)- induced obese mice. Genetic or pharmacological inhibition of the N-formyl peptide receptor Fpr1 leads to increased insulin levels and improved glucose tolerance, dependent upon glucagon- like peptide-1 (GLP-1). Obese Fpr1-knockout (Fpr1-KO) mice also display an altered microbiome, exemplifying the dynamic relationship between host metabolism and microbiota.
    [Show full text]
  • Production of Butyric Acid and Hydrogen by Metabolically Engineered Mutants of Clostridium Tyrobutyricum
    PRODUCTION OF BUTYRIC ACID AND HYDROGEN BY METABOLICALLY ENGINEERED MUTANTS OF CLOSTRIDIUM TYROBUTYRICUM DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Xiaoguang Liu, M.S. ***** The Ohio State University 2005 Dissertation committee: Approved by Professor Shang-Tian Yang, Adviser Professor Barbara E Wyslouzil Adviser Professor Hua Wang Department of Chemical Engineering ABSTRACT Butyric acid has many applications in chemical, food and pharmaceutical industries. The production of butyric acid by fermentation has become an increasingly attractive alternative to current petroleum-based chemical synthesis. Clostridium tyrobutyricum is an anaerobic bacterium producing butyric acid, acetic acid, hydrogen and carbon dioxide as its main products. Hydrogen, as an energy byproduct, can add value to the fermentation process. The goal of this project was to develop novel bioprocess to produce butyric acid and hydrogen economically by Clostridial mutants. Conventional fermentation technologies for butyric acid and hydrogen production are limited by low reactor productivity, product concentration and yield. In this project, novel engineered mutants of C. tyrobutyricum were created by gene manipulation and cell adaptation. Fermentation process was also optimized using immobilizing cells in the fibrous-bed bioreactor (FBB) to enhance butyric acid and hydrogen production. First, metabolic engineered mutants with knocked-out acetate formation pathway were created and characterized. Gene inactivation technology was used to delete the genes of phosphotransacetylase (PTA) and acetate kinase (AK), two key enzymes in the acetate-producing pathway of C. tyrobutyricum, through homologous recombination. The metabolic engineered mutants were characterized by Southern hybridization, enzyme assay, protein expression and metabolites production.
    [Show full text]
  • Association of Coffee and Tea Intake with the Oral Microbiome: Results from a Large Cross-Sectional Study
    Author Manuscript Published OnlineFirst on April 27, 2018; DOI: 10.1158/1055-9965.EPI-18-0184 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. 1 Association of coffee and tea intake with the oral microbiome: results from a large cross-sectional study Brandilyn A. Peters,1 Marjorie L. McCullough,2 Mark P. Purdue,3 Neal D. Freedman,3 Caroline Y. Um,2 Susan M. Gapstur,2 Richard B. Hayes,1,4 Jiyoung Ahn1,4 1Division of Epidemiology, Department of Population Health, NYU School of Medicine, New York, NY, USA 2Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA 3Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA 4NYU Perlmutter Cancer Center, New York, NY, USA Running title: Coffee, tea, and the oral microbiome Corresponding author: Jiyoung Ahn (650 1st Avenue, 5th Floor, New York, NY, 10016; phone: 212-263-3390; fax: 212-263-8570; email: [email protected]) Conflict of interest statement: No conflicts of interest to disclose. Downloaded from cebp.aacrjournals.org on September 23, 2021. © 2018 American Association for Cancer Research. Author Manuscript Published OnlineFirst on April 27, 2018; DOI: 10.1158/1055-9965.EPI-18-0184 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. 2 1 ABSTRACT 2 Background: The oral microbiota play a central role in oral health, and possibly in 3 carcinogenesis. Research suggests coffee and tea consumption may have beneficial 4 health effects. We examined the associations of these common beverages with the oral 5 ecosystem in a large cross-sectional study.
    [Show full text]
  • Effect of Fructans, Prebiotics and Fibres on the Human Gut Microbiome Assessed by 16S Rrna-Based Approaches: a Review
    Wageningen Academic Beneficial Microbes, 2020; 11(2): 101-129 Publishers Effect of fructans, prebiotics and fibres on the human gut microbiome assessed by 16S rRNA-based approaches: a review K.S. Swanson1, W.M. de Vos2,3, E.C. Martens4, J.A. Gilbert5,6, R.S. Menon7, A. Soto-Vaca7, J. Hautvast8#, P.D. Meyer9, K. Borewicz2, E.E. Vaughan10* and J.L. Slavin11 1Division of Nutritional Sciences, University of Illinois at Urbana-Champaign,1207 W. Gregory Drive, Urbana, IL 61801, USA; 2Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, the Netherlands; 3Human Microbiome Research Programme, Faculty of Medicine, University of Helsinki, Haartmaninkatu 3, P.O. Box 21, 00014, Helsinki, Finland; 4Department of Microbiology and Immunology, University of Michigan, 1150 West Medical Center Drive, Ann Arbor, MI 48130, USA; 5Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL 60637, USA; 6Bioscience Division, Argonne National Laboratory, 9700 S Cass Ave, Lemont, IL 60439, USA; 7The Bell Institute of Health and Nutrition, General Mills Inc., 9000 Plymouth Ave N, Minneapolis, MN 55427, USA; 8Division Human Nutrition, Department Agrotechnology and Food Sciences, P.O. Box 17, 6700 AA, Wageningen University; 9Nutrition & Scientific Writing Consultant, Porfierdijk 27, 4706 MH Roosendaal, the Netherlands; 10Sensus (Royal Cosun), Oostelijke Havendijk 15, 4704 RA, Roosendaal, the Netherlands; 11Department of Food Science and Nutrition, University of Minnesota, 1334 Eckles Ave, St. Paul, MN 55108, USA; [email protected]; #Emeritus Professor Received: 27 May 2019 / Accepted: 15 December 2019 © 2020 Wageningen Academic Publishers OPEN ACCESS REVIEW ARTICLE Abstract The inherent and diverse capacity of dietary fibres, nondigestible oligosaccharides (NDOs) and prebiotics to modify the gut microbiota and markedly influence health status of the host has attracted rising interest.
    [Show full text]
  • Human Microbiota Reveals Novel Taxa and Extensive Sporulation Hilary P
    OPEN LETTER doi:10.1038/nature17645 Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation Hilary P. Browne1*, Samuel C. Forster1,2,3*, Blessing O. Anonye1, Nitin Kumar1, B. Anne Neville1, Mark D. Stares1, David Goulding4 & Trevor D. Lawley1 Our intestinal microbiota harbours a diverse bacterial community original faecal sample and the cultured bacterial community shared required for our health, sustenance and wellbeing1,2. Intestinal an average of 93% of raw reads across the six donors. This overlap was colonization begins at birth and climaxes with the acquisition of 72% after de novo assembly (Extended Data Fig. 2). Comparison to a two dominant groups of strict anaerobic bacteria belonging to the comprehensive gene catalogue that was derived by culture-independent Firmicutes and Bacteroidetes phyla2. Culture-independent, genomic means from the intestinal microbiota of 318 individuals4 found that approaches have transformed our understanding of the role of the 39.4% of the genes in the larger database were represented in our cohort human microbiome in health and many diseases1. However, owing and 73.5% of the 741 computationally derived metagenomic species to the prevailing perception that our indigenous bacteria are largely identified through this analysis were also detectable in the cultured recalcitrant to culture, many of their functions and phenotypes samples. remain unknown3. Here we describe a novel workflow based on Together, these results demonstrate that a considerable proportion of targeted phenotypic culturing linked to large-scale whole-genome the bacteria within the faecal microbiota can be cultured with a single sequencing, phylogenetic analysis and computational modelling that growth medium.
    [Show full text]
  • Effects of High Forage/Concentrate Diet on Volatile Fatty Acid
    animals Article Effects of High Forage/Concentrate Diet on Volatile Fatty Acid Production and the Microorganisms Involved in VFA Production in Cow Rumen Lijun Wang 1,2, Guangning Zhang 2, Yang Li 2 and Yonggen Zhang 2,* 1 College of Animal Science and Technology, Qingdao Agricultural university, No. 700 of Changcheng Road, Qingdao 266000, China; [email protected] 2 College of Animal Science and Technology, Northeast Agricultural University, No. 600 of Changjiang Road, Harbin 150030, China; [email protected] (G.Z.); [email protected] (Y.L.) * Correspondence: [email protected]; Tel./Fax: +86-451-5519-0840 Received: 15 January 2020; Accepted: 28 January 2020; Published: 30 January 2020 Simple Summary: The rumen is well known as a natural bioreactor for highly efficient degradation of fibers, and rumen microbes play an important role on fiber degradation. Carbohydrates are fermented by a variety of bacteria in the rumen and transformed into volatile fatty acids (VFAs) by the corresponding enzymes. However, the content of forage in the diet affects the metabolism of cellulose degradation and VFA production. Therefore, we combine metabolism and metagenomics to explore the effects of High forage/concentrate diets and sampling time on enzymes and microorganisms involved in the metabolism of fiber and VFA in cow rumen. This study showed that propionate formation via the succinic pathway, in which succinate CoA synthetase (EC 6.2.1.5) and propionyl CoA carboxylase (EC 2.8.3.1) were key enzymes. Butyrate formation via the succinic pathway, in which phosphate butyryltransferase (EC 2.3.1.19), butyrate kinase (EC 2.7.2.7) and pyruvate ferredoxin oxidoreductase (EC 1.2.7.1) are the important enzymes.
    [Show full text]
  • Anaerostipes Caccae Gen. Nov., Sp. Nov., a New Saccharolytic, Acetate-Utilising, Butyrate-Producing Bacterium from Human Faeces
    System. Appl. Microbiol. 25, 46–51 (2002) © Urban & Fischer Verlag http://www.urbanfischer.de/journals/sam Anaerostipes caccae gen. nov., sp. nov., a New Saccharolytic, Acetate-utilising, Butyrate-producing Bacterium from Human Faeces ANDREAS SCHWIERTZ1, GEORGINA L. HOLD2, SYLVIA H. DUNCAN2, BÄRBEL GRUHL1, MATTHEW D. COLLINS3, PAUL A. LAWSON3, HARRY J. FLINT2 and MICHAEL BLAUT1 1Department of Gastrointestinal Microbiology, German Institute of Human Nutrition, Bergholz-Rehbrücke, Germany 2Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen, UK 3School of Food Biosciences, University of Reading, Reading, UK Received January 28, 2002 Summary Two strains of a previously undescribed Eubacterium-like bacterium were isolated from human faeces. The strains are Gram-variable, obligately anaerobic, catalase negative, asporogenous rod-shaped cells which produced acetate, butyrate and lactate as the end products of glucose metabolism. The two iso- lates displayed 99.9% 16S rRNA gene sequence similarity to each other and treeing analysis demonstrat- ed the faecal isolates are far removed from Eubacterium sensu stricto and that they represent a new sub- line within the Clostridium coccoides group of organisms. Based on phenotypic and phylogenetic crite- ria, it is proposed that the two strains from faeces be classified as a new genus and species, Anaerostipes caccae. The type strain of Anaerostipes caccae is NCIMB 13811T (= DSM 14662T). Key words: Anaerostipes caccae – 16S rRNA – taxonomy – phylogeny – human faeces Introduction The human intestinal tract harbours an immense diver- displayed a high degree of relatedness (16S rRNA) to the sity of bacteria and the total number of resident bacteria butyrate-producing strain L1-92 described by BARCENILLA has been estimated to reach 1014 cells (SAVAGE, 1977; SUAU et al.
    [Show full text]
  • Supplemental Table S1: Comparison of the Deleted Genes in the Genome-Reduced Strains
    Supplemental Table S1: Comparison of the deleted genes in the genome-reduced strains Legend 1 Locus tag according to the reference genome sequence of B. subtilis 168 (NC_000964) Genes highlighted in blue have been deleted from the respective strains Genes highlighted in green have been inserted into the indicated strain, they are present in all following strains Regions highlighted in red could not be deleted as a unit Regions highlighted in orange were not deleted in the genome-reduced strains since their deletion resulted in severe growth defects Gene BSU_number 1 Function ∆6 IIG-Bs27-47-24 PG10 PS38 dnaA BSU00010 replication initiation protein dnaN BSU00020 DNA polymerase III (beta subunit), beta clamp yaaA BSU00030 unknown recF BSU00040 repair, recombination remB BSU00050 involved in the activation of biofilm matrix biosynthetic operons gyrB BSU00060 DNA-Gyrase (subunit B) gyrA BSU00070 DNA-Gyrase (subunit A) rrnO-16S- trnO-Ala- trnO-Ile- rrnO-23S- rrnO-5S yaaC BSU00080 unknown guaB BSU00090 IMP dehydrogenase dacA BSU00100 penicillin-binding protein 5*, D-alanyl-D-alanine carboxypeptidase pdxS BSU00110 pyridoxal-5'-phosphate synthase (synthase domain) pdxT BSU00120 pyridoxal-5'-phosphate synthase (glutaminase domain) serS BSU00130 seryl-tRNA-synthetase trnSL-Ser1 dck BSU00140 deoxyadenosin/deoxycytidine kinase dgk BSU00150 deoxyguanosine kinase yaaH BSU00160 general stress protein, survival of ethanol stress, SafA-dependent spore coat yaaI BSU00170 general stress protein, similar to isochorismatase yaaJ BSU00180 tRNA specific adenosine
    [Show full text]
  • 000572305300015.Pdf(1.52
    www.nature.com/scientificreports OPEN Compositional and functional diferences of the mucosal microbiota along the intestine of healthy individuals Stefania Vaga1,15, Sunjae Lee1,15, Boyang Ji2, Anna Andreasson3,4,5, Nicholas J. Talley6, Lars Agréus7, Gholamreza Bidkhori1, Petia Kovatcheva‑Datchary8,9, Junseok Park10, Doheon Lee10, Gordon Proctor1, Stanislav Dusko Ehrlich11, Jens Nielsen2,12*, Lars Engstrand13* & Saeed Shoaie1,14* Gut mucosal microbes evolved closest to the host, developing specialized local communities. There is, however, insufcient knowledge of these communities as most studies have employed sequencing technologies to investigate faecal microbiota only. This work used shotgun metagenomics of mucosal biopsies to explore the microbial communities’ compositions of terminal ileum and large intestine in 5 healthy individuals. Functional annotations and genome‑scale metabolic modelling of selected species were then employed to identify local functional enrichments. While faecal metagenomics provided a good approximation of the average gut mucosal microbiome composition, mucosal biopsies allowed detecting the subtle variations of local microbial communities. Given their signifcant enrichment in the mucosal microbiota, we highlight the roles of Bacteroides species and describe the antimicrobial resistance biogeography along the intestine. We also detail which species, at which locations, are involved with the tryptophan/indole pathway, whose malfunctioning has been linked to pathologies including infammatory bowel disease. Our
    [Show full text]