Protective Role of the Vulture Facial and Gut Microbiomes Aid Adaptation to Scavenging

Total Page:16

File Type:pdf, Size:1020Kb

Protective Role of the Vulture Facial and Gut Microbiomes Aid Adaptation to Scavenging bioRxiv preprint doi: https://doi.org/10.1101/211490; this version posted October 30, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Protective role of the vulture facial and gut microbiomes aid adaptation to 2 scavenging 3 M. Lisandra Zepeda Mendoza1*, Gary R. Graves2, Michael Roggenbuck3, Karla Manzano Vargas1,4, 4 Lars Hestbjerg Hansen5, Søren Brunak6, M. Thomas P. Gilbert1, 7*, Thomas Sicheritz-Pontén6* 5 6 1 Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen. Øster 7 Voldgade 5-7, 1350 Copenhagen K, Denmark. 8 2 Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 9 Division of Birds, 20013 Washington, DC, USA. 10 3 Department for Bioinformatics and Microbe Technology, Novozymes A/S, 2880 Bagsværd, 11 Denmark. 12 4 Undergraduate Program on Genomic Sciences, Center for Genomic Sciences, National 13 Autonomous University of Mexico, Av. Universidad s/n Col. Chamilpa, 62210 Cuernavaca, Morelos, 14 Mexico. 15 5 Section for Microbiology and Biotechnology, Department of Environmental Science, Aarhus 16 University, Frederiksborgvej 399, 4000 Roskilde, Denmark. 17 6 Center for Biological Sequence Analysis, Department of Bio and Health Informatics, Technical 18 University of Denmark, Anker Engelunds Vej 1 Bygning 101A, 2800 Kgs. Lyngby, Denmark. 19 7 Norwegian University of Science and Technology, University Museum, 7491 Trondheim, Norway. 20 *Correspondence to: Thomas Sicheritz-Pontén, e-mail: [email protected], M. Thomas P. Gilbert, 21 e-mail: [email protected], and M. Lisandra Zepeda Mendoza, e-mail: [email protected] 22 23 24 1 bioRxiv preprint doi: https://doi.org/10.1101/211490; this version posted October 30, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 25 Abstract 26 Background: Vultures have adapted the remarkable ability to feed on carcasses that may contain 27 microorganisms that would be pathogenic to most other animals. The holobiont concept suggests that 28 the genetic basis of such adaptation may not only lie within their genomes, but additionally in their 29 associated microbes. To explore this, we generated shotgun DNA sequencing datasets of the facial 30 and gut microbiomes from the black and turkey vultures. We characterized i) the functional potential 31 and taxonomic diversity of their microbiomes, ii) the potential pathogenic challenges they face, and 32 iii) elements in the microbiome that could play a protective role to the vulture’s face and gut. 33 Results: We found elements involved in diseases, such as periodontitis and pneumonia (more 34 abundant in the face), and gas gangrene and food poisoning (more abundant in the gut). Interestingly, 35 we found taxa and functions with potential for playing health beneficial roles, such as antilisterial 36 bacteria in the gut, and genes for the production of antiparasites and antiinsectisides in the face. Based 37 on the identified phages, we suggest that phages aid in the control, and possibly elimination as in 38 phage therapy, of microbes reported as pathogenic to a variety of species. Interestingly, we also 39 identified Adineta vaga in the gut, an invertebrate that feeds on dead bacteria and protozoans, 40 suggesting a defensive predatory mechanism. Finally, we suggest a colonization resistance role 41 though biofilm formation played by Fusobacteria and Clostridia in the gut. 42 Conclusions: Our results highlight the importance of complementing genomic analyses with 43 metagenomics in order to obtain a clearer understanding of the host-microbial alliance and show the 44 importance of microbiome-mediated health protection for adaptation to extreme diets, such as 45 scavenging. 46 47 Keywords: Microbiome, diet specialization, scavenging, colonization resistance, pathogens, vulture, 48 metagenomics. 2 bioRxiv preprint doi: https://doi.org/10.1101/211490; this version posted October 30, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 49 50 Background 51 Vultures are scavengers whose global populations are under serious threats, and a better 52 understanding of various aspects for their biology are necessary [1,2]. Vultures are known as nature’s 53 clean-up crew as they feed on muscles and viscera from carcasses of animals that have died mainly 54 from malnutrition, accidents, and natural or infectious diseases, thus are expected to carry pathogens 55 such as those causing anthrax, tuberculosis, brucellosis, etc. [3]. Carcasses are a very nutrient-rich 56 resource and it has been speculated that the release of toxins and pathogenicity genes in the carcass 57 microbiome are part of a microbial strategy for outcompeting other microbes [4,5]. The main 58 colonizers of a carcass are microbes originating from the normal flora of the dead animal, which 59 might turn pathogenic in the carcass environment [6], as well as soil-dwelling bacteria, nematodes, 60 fungi and insects [7]. In spite of the potentially serious health implications posed by their 61 consumption, the pathogenic repertoire of the gut of these species of birds has not been fully 62 characterized in relation to their possible implications in the environment. Thus, one of the most 63 intriguing aspects of vulture biology is how they protect themselves against the health challenges 64 posed by their dietary source. Physiologic, genetic and genomic analyses of different species of 65 vultures have explored this aspect and identified genes associated to respiration, immunity and gastric 66 secretion as candidates for the adaptation to its scavenging diet [8,9]. 67 With the genomic revolution it has become apparent that besides genomic changes, host-associated 68 microbiota play an important role in diet specialization across vertebrates [10] and that the gut 69 microbiome may play highly relevant yet unexplored role in diet-driven speciation [11]. The gut 70 microbiome is related to digestion traits, such as energy harvest, nutrient acquisition, and intestinal 71 homeostasis [12], among other phenotypes related to the immune and neuroendocrine systems [13– 72 15]. Furthermore, the role of the microbiome in health protection to the host has also been 3 bioRxiv preprint doi: https://doi.org/10.1101/211490; this version posted October 30, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 73 demonstrated [16,17], and disorders in it lead to diseases such as irritable bowel syndrome, 74 inflammatory bowel disease, obesity and diabetes [18–20]. In light of the key roles that host- 75 microbiome relationships can play in adaptation, it has been acknowledged that genomic adaptations 76 alone may not provide the full answer to the vulture adaptations for scavenging [8]. However, neither 77 the complete microbial taxonomic diversity (including non-bacterial microbes) nor the gene 78 catalogue of any vulture species’ face and gut microbiomes have been examined for their protective 79 role against microbes that would normally pose serious health risks for other non-scavenging 80 vertebrate species. 81 In order to evaluate the protective role of the vulture’s facial and gut microbiome, we generated 82 metagenomic datasets from facial swabs and gut samples for two species of New World vultures, the 83 black vulture (Coragyps atratus) and the turkey vulture (Cathartes aura), and performed 84 metagenomic taxonomic and functional analyses. We identified a wide variety of taxa and genes that 85 would cause serious diseases, e.g. sepsis, gangrene and food poisoning, to animals without protection 86 provided by a specialized scavenging microbiome. Such protection could consist of health defence 87 elements not only from bacterial probiotics, but also from phages and predatory eukaryotes. Our 88 results suggest that the vulture’s microbiota plays a significant health-protective role in its adaptation 89 to a scavenging diet. 90 91 Methods 92 Sampling method and DNA sequencing 93 We analysed a subset of the sample set used by Roggenbuck et al. [21]. Briefly, the vultures were 94 collected over a period of several days in Tenessee, USA. Coragyps atratus were live-trapped at deer 95 carcasses and then transported to a central facility within a couple of hours of trapping. They were 96 then euthanized with CO2, necropsied, and sampled within 30-45 minutes of death. Cathartes aura 4 bioRxiv preprint doi: https://doi.org/10.1101/211490; this version posted October 30, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 97 vultures were shot at roosts, bagged individually, and transported to the processing facility where 98 they were refrigerated 2-6 hours before necropsy and sampling. The samples were kept in RNAlater 99 and DNA was extracted and the shotgun libraries for HiSeq PE 100 prepared using the Nextera library 100 building kit following the manufacturer’s instructions, as in Roggenbuck et al. [21]. We used a total 101 of 22 turkey vulture (Cathartes aura) and 25 black vulture (Coragyps atratus) large intestine samples, 102 and 16 turkey vulture and 17 black vulture facial samples. 103 Data processing 104 Two pipelines were used for the processing of the raw reads. In the first approach, we removed 105 adapter sequences and bases with quality <15 using Trimmomatic v0.32 [22]. Afterwards, in order to 106 filter out non-bacterial reads of avian, human, and Phi phage origin, the datasets were mapped against 107 the bird genomes dataset of the avian phylogenomic project [23] (which includes the turkey vulture 108 genome), the human (hg19) and the Phi phage genomes, and only the non-mapping reads were kept.
Recommended publications
  • Structure and Dynamics of the Microbial Communities Underlying the Carboxylate Platform for Biofuel Production
    Structure and dynamics of the microbial communities underlying the carboxylate platform for biofuel production E.B. Hollister 1, A.K. Forrest 2, H.H. Wilkinson 3, D.J. Ebbole 3, S.A. Malfatti 4, S.G. Tringe 4, M.T. Holtzapple 2, T.J. Gentry 1 1 Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA 77843-2474 2 Department of Chemical Engineering, Texas A&M University, College Station, TX, USA 77843-3122 3 Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX USA 77843-2132 4 DOE Joint Genome Institute, Walnut Creek, CA, USA 94598 July 31, 2010 ACKNOWLEDGMENT The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231 DISCLAIMER This document was prepared as an account of work sponsored by the United States Government. While this document is believed to contain correct information, neither the United States Government nor any agency thereof, nor The Regents of the University of California, nor any of their employees, makes any warranty, express or implied, or assumes any legal responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by its trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or The Regents of the University of California.
    [Show full text]
  • Supplementary Materials
    SUPPLEMENTARY MATERIALS Table S1. Chemical characteristics of the two digestate forms (SD and WD). Values quoted are expressed as % of air-dry digestate (means followed by standard error in brackets). References for the employed methods used for determination of each chemical characteristic is also reported. SD WD Reference Org C % 44.4 (0.33) 1.1 (0.01) [81] Tot N % 1.4 (0.01) 0.4 (0.01) [82] C/N 31.4 (0.17) 3.1 (0.04) NH4-N % n.d 0.2 (0.00) [83] K % 1.7 (0.00) n.d. [84] P % 0.9 (0.01) n.d. [84] S % 0.23 (0.02) n.d. [85] SD = solid digestate; WD = whole digestate. Table S2. Soil physical and chemical characteristics at the beginning of trial (t0) (means from 9 observations followed by standard errors in brackets). Clay (%) 41.9 (1.22) Silt (%) 47.8 (2.13) Moisture (%) 24.46 (1.24) Bulk density (g cm-3) 1.39 (0.04) pH 8.3 (0) CaCO3 (%) 11.4 (0.7) TOC (g kg-1) 12.8 (0.3) TN (g kg-1) 1.4 (0) C/N 9.4 (0.3) CEC (cmol(+) kg-1) 21.0 (0.7) Exchangeable Bases (mg kg-1) K 278.7 (8.0) Na 22.0 (3.0) Mg 201.7 (25.6) Ca 3718.6 (176.3) Available Microelements (mg kg-1) Cu 28.0 (5.0) Zn 1.7 (0.2) Fe 15.4 (0.5) Mn 16.3 (0.5) TOC = total organic C; TN = total N; CEC = cation exchange capacity Table S3.
    [Show full text]
  • WO 2018/064165 A2 (.Pdf)
    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2018/064165 A2 05 April 2018 (05.04.2018) W !P O PCT (51) International Patent Classification: Published: A61K 35/74 (20 15.0 1) C12N 1/21 (2006 .01) — without international search report and to be republished (21) International Application Number: upon receipt of that report (Rule 48.2(g)) PCT/US2017/053717 — with sequence listing part of description (Rule 5.2(a)) (22) International Filing Date: 27 September 2017 (27.09.2017) (25) Filing Language: English (26) Publication Langi English (30) Priority Data: 62/400,372 27 September 2016 (27.09.2016) US 62/508,885 19 May 2017 (19.05.2017) US 62/557,566 12 September 2017 (12.09.2017) US (71) Applicant: BOARD OF REGENTS, THE UNIVERSI¬ TY OF TEXAS SYSTEM [US/US]; 210 West 7th St., Austin, TX 78701 (US). (72) Inventors: WARGO, Jennifer; 1814 Bissonnet St., Hous ton, TX 77005 (US). GOPALAKRISHNAN, Vanch- eswaran; 7900 Cambridge, Apt. 10-lb, Houston, TX 77054 (US). (74) Agent: BYRD, Marshall, P.; Parker Highlander PLLC, 1120 S. Capital Of Texas Highway, Bldg. One, Suite 200, Austin, TX 78746 (US). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW.
    [Show full text]
  • Comparison of Sampling Techniques and Different Media for The
    Systematic and Applied Microbiology 42 (2019) 481–487 Contents lists available at ScienceDirect Systematic and Applied Microbiology jou rnal homepage: http://www.elsevier.com/locate/syapm Comparison of sampling techniques and different media for the enrichment and isolation of cellulolytic organisms from biogas fermentersଝ a a b a,∗ Regina Rettenmaier , Carina Duerr , Klaus Neuhaus , Wolfgang Liebl , a,c,∗ Vladimir V. Zverlov a Department of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany b Core Facility Microbiome/NGS, ZIEL — Institute for Food & Health, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany c Institute of Molecular Genetics, RAS, Kurchatov Sq. 2, 123128 Moscow, Russia a r t i c l e i n f o a b s t r a c t Article history: Biogas plants achieve its highest yield on plant biomass only with the most efficient hydrolysis of cellulose. Received 27 March 2019 This is driven by highly specialized hydrolytic microorganisms, which we have analyzed by investigating Received in revised form 15 May 2019 enrichment strategies for the isolation of cellulolytic bacteria out of a lab-scale biogas fermenter. We Accepted 17 May 2019 compared three different cultivation media as well as two different inoculation materials: Enrichment on filter paper in nylon bags (in sacco) or raw digestate. Next generation sequencing of the V3/V4 region Keywords: of the bacterial 16S rRNA of metagenomic DNA from six different enrichment cultures, each in biolog- Biogas fermenter ical triplicates, revealed an average richness of 48 different OTU’s with an average evenness of 0.3 in Cellulose degradation each sample.
    [Show full text]
  • André Luis Alves Neves 6
    Elucidating the role of the rumen microbiome in cattle feed efficiency and its 1 potential as a reservoir for novel enzyme discovery 2 3 by 4 5 André Luis Alves Neves 6 7 8 9 10 11 12 A thesis submitted in partial fulfillment of the requirements for the degree of 13 14 15 Doctor of Philosophy 16 17 in 18 19 Animal Science 20 21 22 23 24 25 Department of Agricultural, Food and Nutritional Science 26 University of Alberta 27 28 29 30 31 32 33 34 35 36 37 © André Luis Alves Neves, 2019 38 39 40 Abstract 1 2 The rapid advances in omics technologies have led to a tremendous progress in our 3 understanding of the rumen microbiome and its influence on cattle feed efficiency. 4 However, significant gaps remain in the literature concerning the driving forces that 5 influence the relationship between the rumen microbiota and host individual variation, and 6 how their interactive effects on animal productivity contribute to the identification of cattle 7 with improved feed efficiency. Furthermore, little is known about the impact of mRNA- 8 based metatranscriptomics on the analysis of rumen taxonomic profiles, and a strategy 9 for the discovery of lignocellulolytic enzymes through the targeted functional profiling of 10 carbohydrate-active enzymes (CAZymes) remains to be developed. Study 1 investigated 11 the dynamics of rumen microorganisms in cattle raised under different feeding regimens 12 (forage vs. grain) and studied the relationship among the abundance of these 13 microorganisms, host individuality and the diet. To examine host individual variation in 14 the rumen microbial abundance following dietary switches, hosts were grouped based on 15 the magnitude of microbial population shift using log2-fold change (log2-fc) in the copy 16 numbers of bacteria, archaea, protozoa and fungi.
    [Show full text]
  • From Genotype to Phenotype: Inferring Relationships Between Microbial Traits and Genomic Components
    From genotype to phenotype: inferring relationships between microbial traits and genomic components Inaugural-Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakult¨at der Heinrich-Heine-Universit¨atD¨usseldorf vorgelegt von Aaron Weimann aus Oberhausen D¨usseldorf,29.08.16 aus dem Institut f¨urInformatik der Heinrich-Heine-Universit¨atD¨usseldorf Gedruckt mit der Genehmigung der Mathemathisch-Naturwissenschaftlichen Fakult¨atder Heinrich-Heine-Universit¨atD¨usseldorf Referent: Prof. Dr. Alice C. McHardy Koreferent: Prof. Dr. Martin J. Lercher Tag der m¨undlichen Pr¨ufung: 24.02.17 Selbststandigkeitserkl¨ arung¨ Hiermit erkl¨areich, dass ich die vorliegende Dissertation eigenst¨andigund ohne fremde Hilfe angefertig habe. Arbeiten Dritter wurden entsprechend zitiert. Diese Dissertation wurde bisher in dieser oder ¨ahnlicher Form noch bei keiner anderen Institution eingereicht. Ich habe bisher keine erfolglosen Promotionsversuche un- ternommen. D¨usseldorf,den . ... ... ... (Aaron Weimann) Statement of authorship I hereby certify that this dissertation is the result of my own work. No other person's work has been used without due acknowledgement. This dissertation has not been submitted in the same or similar form to other institutions. I have not previously failed a doctoral examination procedure. Summary Bacteria live in almost any imaginable environment, from the most extreme envi- ronments (e.g. in hydrothermal vents) to the bovine and human gastrointestinal tract. By adapting to such diverse environments, they have developed a large arsenal of enzymes involved in a wide variety of biochemical reactions. While some such enzymes support our digestion or can be used for the optimization of biotechnological processes, others may be harmful { e.g. mediating the roles of bacteria in human diseases.
    [Show full text]
  • General Intoduction
    UNIVERSITÁ DEGLI STUDI DI CATANIA Dipartimento di Agricoltura, Alimentazione e Ambiente PhD Research in Food Production and Technology- XXVIII cycle Alessandra Pino Lactobacillus rhamnosus: a versatile probiotic species for foods and human applications Doctoral thesis Promoter Prof. C.L. Randazzo Co-promoter Prof. C. Caggia TRIENNIUM 2013-2015 Science knows no country, because knowledge is the light that illuminated the word 2 TABLE OF CONTENTS CHAPTER 1 General introduction and thesis outline 1 CHAPTER 2 Lactobacillus rhamnosus in Pecorino Siciliano 36 production and ripening CHAPTER 3 Lactobacillus rhamnosus in table olives 80 production CHAPTER 4 Lactobacillus rhamnosus GG for Bacterial 115 Vaginosis treatment CHAPTER 5 Lactobacillus rhamnosus GG supplementation 159 in Systemic Nickel allergy Syndrome patients APPENDICES List of figures 212 List of tables 216 List of pubblications 218 Poster presentations 220 Acknowledgements 221 Chapter 1 General introduction and thesis outline 4 Chapter 1 INTRODUCTION The term probiotic is a relatively new word meaning “for life”, used to designate microorganisms that are associated with the beneficial effects for humans and animals. These microorganisms contribute to intestinal microbial balance and play an important role in maintaining health. Several definitions of “probiotic” have been used over the years but the one derived by the Food and Agriculture Organization of the United Nations/World Health Organization (2001) (29), endorsed by the International Scientific Association for Probiotics
    [Show full text]
  • Microbial Diversity of a Mesophilic Hydrogen-Producing Sludge
    Appl Microbiol Biotechnol (2002) 58:112–118 DOI 10.1007/s00253-001-0865-8 ORIGINAL PAPER H. H. P. Fang · T. Zhang · H. Liu Microbial diversity of a mesophilic hydrogen-producing sludge Received: 21 July 2001 / Revised: 25 September 2001 / Accepted: 5 October 2001 / Published online: 22 November 2001 © Springer-Verlag 2001 Abstract A hydrogen-producing sludge degraded 99% compounds and may be recovered from wastewater of glucose at 36 °C and pH 5.5, producing a methane- (Ueno et al. 1996) or solid waste (Lay et al. 1999; free biogas (comprising 64% hydrogen) and an effluent Mizuno et al. 1997), using mixed cultures by suppressing comprising mostly butyrate, acetate, and ethanol. The the activity of hydrogenotrophic methanogens. However, –1 yield was 0.26 l H2 g glucose and the production rate little information is available on the hydrogen-producing –1 per gram of volatile suspended solids was 4.6 l H2 day . microbial community. A 16S rDNA library was constructed from the sludge for Traditionally, microbes are identified by isolating in- microbial species determination. A total of 96 clones dividual cultures and examining their physiological, bio- were selected for plasmids recovery, screened by dena- chemical, and morphological characteristics. Clostridium turing gradient gel electrophoresis, and sequenced for was found using these methods as the hydrogen-produc- rDNA. Based on the phylogenetic analysis of the rDNA ing bacterium (HPB) in a mixed culture (Lay 2000). sequences, 64.6% of all the clones were affiliated with However, such an identification is often unreliable. First, three Clostridium species (Clostridiaceae), 18.8% with microbes may not be properly isolated from the artificial Enterobacteriaceae, and 3.1% with Streptococcus bovis growth medium.
    [Show full text]
  • Effects of Heat Treatment on Hydrogen Production Potential and Microbial Community of Thermophilic Compost Enrichment Cultures
    1 1 Effects of heat treatment on hydrogen production potential 2 and microbial community of thermophilic compost 3 enrichment cultures 4 5 Marika E. Nissiläa,*, Hanne P. Tähtib, Jukka A. Rintalab, Jaakko A. Puhakkaa 6 7 a Department of Chemistry and Bioengineering, Tampere University of Technology, 8 Tampere, Finland. 9 b Department of Biological and Environmental Science, University of Jyväskylä, 10 Jyväskylä, Finland 11 * Corresponding author. Address: Tampere University of Technology, Department of 12 Chemistry and Bioengineering, P.O. Box 541, FIN-33101, Tampere, Finland; Tel.: 13 +358 40 198 1140; Fax: +358 3 3115 2869; e- mail: [email protected]. 14 15 Abstract 16 17 Cellulosic plant and waste materials are potential resources for fermentative hydrogen 18 production. In this study, hydrogen producing, cellulolytic cultures were enriched from 19 compost material at 52, 60 and 70ºC. Highest cellulose degradation and highest H2 yield -1 -1 20 were 57 % and 1.4 mol-H2 mol-hexose (2.4 mol-H2 mol-hexose-degraded ), 21 respectively, obtained at 52°C with the heat-treated (80°C for 20 min) enrichment 22 culture. Heat-treatments as well as the sequential enrichment decreased the diversity of 23 microbial communities. The enrichments contained mainly bacteria from families 24 Thermoanaerobacteriaceae and Clostridiaceae, from which a bacterium closely related 2 25 to Thermoanaerobium thermosaccharolyticum was mainly responsible for hydrogen 26 production and bacteria closely related to Clostridium cellulosi and Clostridium 27 stercorarium were responsible for cellulose degradation. 28 29 Keywords: Dark fermentation, cellulose, mixed culture, thermophilic, 30 Thermoanaerobium thermosaccharolyticum 31 32 1 Introduction 33 34 Increasing energy demand and global warming that is associated with the increasing use 35 of fossil fuels increase the demand to produce clean, renewable energy.
    [Show full text]
  • Gallstone Disease, Obesity and the Firmicutes/Bacteroidetes Ratio As a Possible Biomarker of Gut Dysbiosis
    Journal of Personalized Medicine Review Gallstone Disease, Obesity and the Firmicutes/Bacteroidetes Ratio as a Possible Biomarker of Gut Dysbiosis Irina N. Grigor’eva Laboratory of Gastroenterology, Research Institute of Internal and Preventive Medicine-Branch of The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences, Novosibirsk 630089, Russia; niitpm.offi[email protected]; Tel.: +7-9137520702 Abstract: Obesity is a major risk factor for developing gallstone disease (GSD). Previous studies have shown that obesity is associated with an elevated Firmicutes/Bacteroidetes ratio in the gut microbiota. These findings suggest that the development of GSD may be related to gut dysbiosis. This review presents and summarizes the recent findings of studies on the gut microbiota in patients with GSD. Most of the studies on the gut microbiota in patients with GSD have shown a significant increase in the phyla Firmicutes (Lactobacillaceae family, genera Clostridium, Ruminococcus, Veillonella, Blautia, Dorea, Anaerostipes, and Oscillospira), Actinobacteria (Bifidobacterium genus), Proteobacteria, Bacteroidetes (genera Bacteroides, Prevotella, and Fusobacterium) and a significant decrease in the phyla Bacteroidetes (family Muribaculaceae, and genera Bacteroides, Prevotella, Alistipes, Paludibacter, Barnesiella), Firmicutes (genera Faecalibacterium, Eubacterium, Lachnospira, and Roseburia), Actinobacteria (Bifidobacterium genus), and Proteobacteria (Desulfovibrio genus). The influence of GSD on microbial diversity is not clear. Some studies report that GSD reduces microbial diversity in the bile, whereas others suggest the increase in microbial diversity in the bile of patients with GSD. The phyla Proteobacteria (especially family Enterobacteriaceae) and Firmicutes (Enterococcus genus) are most commonly detected in the bile of patients with GSD. On the other hand, the composition of bile microbiota in patients with GSD shows considerable inter-individual variability.
    [Show full text]
  • MICROBIAL Cr(VI) REDUCTION: ROLE of ELECTRON DONORS, ACCEPTORS, and MECHANISMS, with SPECIAL EMPHASIS on CLOSTRIDIUM Spp
    MICROBIAL Cr(VI) REDUCTION: ROLE OF ELECTRON DONORS, ACCEPTORS, AND MECHANISMS, WITH SPECIAL EMPHASIS ON CLOSTRIDIUM spp. By KANIKA SHARMA A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2002 Copyright 2002 by Kanika Sharma For my parents, whose support and understanding has helped culminate my dream into a reality. ACKNOWLEDGMENTS I am grateful to my mentor, Dr. Andrew V. Ogram, for excellent supervision during the course of this dissertation. He has truly been a great source of inspiration, insight, and input. The knowledge he has imparted, and the patience he has displayed was vital to completing this study. I am thankful for the immense encouragement and financial support that he graciously provided during this study. I would like to express my sincere gratitude to the committee members, Drs. K. Hatfield, L. O. Ingram, K. R. Reddy, and R. D. Rhue, for each contributing in special and meaningful ways to my personal development and academic success. I also thank Drs. W. Harris, L.T. Ou, and H. Aldrich for all of their advice and help. A special word of thanks is due to Dr. Derek Lovley, and members of his lab at the University of Massachusetts, Amherst, for extending their lab facilities so that I might learn various anaerobic microbial techniques. At this time, I would also like to thank Dr. John Thomas, Bill Reve, and Irene Poyer for all their help with the analytical equipment. I am especially grateful to T.
    [Show full text]
  • Impact of Intestinal Microbiota on Growth and Feed Efficiency
    microorganisms Review Impact of Intestinal Microbiota on Growth and Feed Efficiency in Pigs: A Review Gillian E. Gardiner 1,* , Barbara U. Metzler-Zebeli 2 and Peadar G. Lawlor 3 1 Department of Science, Waterford Institute of Technology, X91 K0EK Co. Waterford, Ireland 2 Unit Nutritional Physiology, Institute of Physiology, Pathophysiology and Biophysics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; [email protected] 3 Teagasc, Pig Development Department, Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy, P61 C996 Co. Cork, Ireland; [email protected] * Correspondence: [email protected]; Tel.: +353-51-302-626 Received: 2 October 2020; Accepted: 25 November 2020; Published: 28 November 2020 Abstract: This review summarises the evidence for a link between the porcine intestinal microbiota and growth and feed efficiency (FE), and suggests microbiota-targeted strategies to improve productivity. However, there are challenges in identifying reliable microbial predictors of host phenotype; environmental factors impact the microbe–host interplay, sequential differences along the intestine result in segment-specific FE- and growth-associated taxa/functionality, and it is often difficult to distinguish cause and effect. However, bacterial taxa involved in nutrient processing and energy harvest, and those with anti-inflammatory effects, are consistently linked with improved productivity. In particular, evidence is emerging for an association of Treponema and methanogens such as Methanobrevibacter in the small and large intestines and Lactobacillus in the large intestine with a leaner phenotype and/or improved FE. Bacterial carbohydrate and/or lipid metabolism pathways are also generally enriched in the large intestine of leaner pigs and/or those with better growth/FE.
    [Show full text]