Comparative Metagenomic Analysis of Microcosm Structures and Lignocellulolytic Enzyme Systems of Symbiotic Biomass-Degrading Consortia

Total Page:16

File Type:pdf, Size:1020Kb

Comparative Metagenomic Analysis of Microcosm Structures and Lignocellulolytic Enzyme Systems of Symbiotic Biomass-Degrading Consortia Comparative metagenomic analysis of microcosm structures and lignocellulolytic enzyme systems of symbiotic biomass-degrading consortia Sarunyou Wongwilaiwalin & Thanaporn Laothanachareon & Wuttichai Mhuantong & Sithichoke Tangphatsornruang & Lily Eurwilaichitr & Yasuo Igarashi & Verawat Champreda Received: 2 October 2012 /Revised: 3 January 2013 /Accepted: 7 January 2013 # Springer-Verlag Berlin Heidelberg 2013 Abstract Decomposition of lignocelluloses by cooperative industrial pulp waste with CMCase, xylanase, and β- microbial actions is an essential process of carbon cycling in glucanase activities in the supernatant. Shotgun pyrosequenc- nature and provides a basis for biomass conversion to fuels ing of the BGC-1 metagenome indicated a markedly high and chemicals in biorefineries. In this study, structurally stable relative abundance of genes encoding for glycosyl hydrolases, symbiotic aero-tolerant lignocellulose-degrading microbial particularly for lignocellulytic enzymes in 26 families. The consortia were obtained from biodiversified microflora pres- enzyme system comprised a unique composition of main- ent in industrial sugarcane bagasse pile (BGC-1), cow rumen chain degrading and side-chain processing hydrolases, domi- fluid (CRC-1), and pulp mill activated sludge (ASC-1) by nated by GH2, 3, 5, 9, 10, and 43, reflecting adaptation of successive subcultivation on rice straw under facultative an- enzyme profiles to the specific substrate. Gene mapping oxic conditions. Tagged 16S rRNA gene pyrosequencing showed metabolic potential of BGC-1 for conversion of bio- revealed that all isolated consortia originated from highly mass sugars to various fermentation products of industrial diverse environmental microflora shared similar composite importance. The symbiotic consortium is a promising simpli- phylum profiles comprising mainly Firmicutes, reflecting fied model for study of multispecies mechanisms on consol- convergent adaptation of microcosm structures, however, with idated bioprocessing and a platform for discovering efficient substantial differences at refined genus level. BGC-1 compris- synergistic enzyme systems for biotechnological application. ing cellulolytic Clostridium and Acetanaerobacterium in sta- ble coexistence with ligninolytic Ureibacillus showed the Keywords Biorefinery . Glycosyl hydrolase . highest capability on degradation of agricultural residues and Lignocellulose . Metagenome . Microbial consortium S. Wongwilaiwalin : T. Laothanachareon : W. Mhuantong : L. Eurwilaichitr : V. Champreda (*) Introduction Enzyme Technology Laboratory, Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology, Lignocellulosic plant biomass is the most abundant organic 113 Thailand Science Park, Klong Luang, Pathum Thani 12120, Thailand carbon reservoir on earth, providing a renewable carbon e-mail: [email protected] source for the chemosphere and the prospective biorefinery industry. Development of carbon neutral biomass conver- S. Tangphatsornruang sion processes has attracted much public interest in recent Genome Institute, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, years as a promising alternative platform for production of Klong Luang, Pathum Thani 12120, Thailand fuels and chemicals, which could reduce the global depen- dence on petroleum (FitzPatrick et al. 2010). Extensive Y. Igarashi research has been conducted to increase our understanding Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, of the complex natural bioconversion of lignocelluloses, Tokyo 113-8657, Japan particularly on degradation of recalcitrant plant biomass, Reproduced from Appl. Microbiol. Biotechnol. DOI 10.1007/s00253-013-4699-y. 163 which is an essential starting step in biorefinery. Insights Culture-independent direct 454 pyrosequencing of envi- into biomass decomposition by means of intricate biological ronmental metagenomes has previously been applied to processes not only provides us a fundamental basis on study diversity and metabolic capabilities of natural biomass essential roles of microbes in maintaining carbon balance decay microbiomes in various environments, e.g., tropical of the eco-system but is also of great interest for future peat swamp forest (Kanokratana et al. 2010), termite gut establishment of viable biorefineries for our sustainable (Warnecke et al. 2007; Nimchua et al. 2011), cow rumen society. (Brulc et al. 2009), and switch grass-adapted compost com- Lignocellulosic materials consist of mainly three different munity (Allgaier et al. 2010). These works illustrate the types of polymers, i.e., cellulose, hemicelluloses, and lignin, highly diversified nature of unexplored plant biomass- which are associated with each other (Fengel and Wegener degrading microbes and their enzymes awaiting discovery 1984). In nature, lignocelluloses are degraded by a complex for biotechnological uses. In this study, comparative analy- multistep process involving cooperative actions of various sis of structurally stable cellulolytic consortia isolated from microorganisms producing a variety of cellulolytic, hemicel- biodiversified microcosms in various environments active in lulolytic, and ligninolytic enzymes that act specifically and plant biomass deconstruction was reported using tagged 16S synergistically to degrade plant biomass. The concept on rRNA gene pyrosequencing, which demonstrated effects of utilization of simplified multispecies consortia, ranging from the enrichment process on shaping of the community struc- dual-species systems to complex microcosms on plant bio- tures. Lignocellulolytic enzyme systems of the consortium mass decomposition, is a promising strategy to achieve high were further explored using shotgun metagenome pyrose- degradation efficiency compared to using a single cellulolytic quencing, which showed the highly enriched nature of gene isolate (Lynd et al. 2002). A number of structurally stable sets encoding a distinct enzyme profile compared with pre- multispecies consortia with high cellulose-degrading activity viously reported plant biomass degrading microbiomes. The have been obtained by successive culture enrichments using work provides the first in-depth analysis of lignocellulolytic agricultural biomass as the sole carbon source under meso- enzyme systems and metabolic potential of a symbiotic and thermophilic conditions. These symbiotic consortia can biomass degrading consortium by metagenomic approaches. efficiently degrade various cellulosic materials, such as agro- This study gives valuable insights into the mechanism in industrial residues, filter paper, cotton, and pulp wastes consolidated lignocellulose degradation and conversion by a (Haruta et al. 2002; Guo et al. 2010; Wongwilaiwalin et al. symbiotic consortium and provides a promising gene min- 2010;Fengetal.2011;Wangetal.2011). A defined cellulose- ing platform for discovery of efficient synergistic enzyme degrading consortium was assembled from microbial isolates systems for biotechnological application. in a mixed culture microcosm (Kato et al. 2004), and study of this simplified microcosm revealed complex metabolic inter- dependences among the community members, which contrib- Materials and methods ute to the consortium stability (Kato et al. 2005, 2008). These symbiotic consortia typically comprise mainly anaerobic cel- Materials lulolytic bacterial taxa in stable coexistence with various non- cellulolytic members, which play important roles in Sources of microflora for preparation of microbial consortia metabolite dependence and environment modification, lead- in this study were collected from (1) sugarcane bagasse ing to enhancement in biomass hydrolysis efficiency of the decomposed soil from an industrial bagasse collection site multispecies systems. Modification of lignocellulose degrad- at the Phu Kheio Bio-Energy factory (Chaiyapoom, ing consortia was first explored by introducing and acclima- Thailand), (2) cow rumen fluid from Holstein cows housed tion of a cellulolytic clostridial strain into the system, which at the Khon Kaen Agriculture and Training Center (Roi Et, showed a way for alteration of the consortium structures and Thailand), and (3) activated sludge from a local soda pulp functions (Narisawa et al. 2007). The conceptual design on mill (Ratchaburi, Thailand). Rice straw and other agricul- development of symbiotic consortia comprising either natural tural by-products used as substrates in enrichment and bio- or engineered members has been recently reported as a prom- mass degradation efficiency analysis were obtained locally. ising approach for the establishment of microbial systems for The agricultural by-products were pretreated with alkali consolidated bioprocessing (Zuroff and Curtis 2012). Thus, (10 % w/v NaOH with 3:1 liquid/solid ratio at 90 °C for these studies indicate potential of the symbiotic microbial 90 min) for partial delignification. The native rice straw consortia, not only as the highly efficient biomass degrading contained 41.90 % cellulose, 34.24 % hemicelluloses, and systems but also for further modification of interspecies met- 22.44 % lignin, while the alkali-treated rice straw comprised abolic flux in designated consortia aiming for direct conver- of 68.69 % cellulose, 19.41 % hemicellulose, and 4.45 % sion of biomass to fuels and chemicals of industrial lignin according to analysis by Technical Association of importance. Pulp and Paper Industry
Recommended publications
  • 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]
  • Variations of the Intestinal Gut Microbiota of Farmed Rainbow Trout, Oncorhynchus Mykiss (Walbaum), Depending on the Infection Status of the Fish"
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by IRTA Pubpro This is the peer reviewed version of the following article: Parshukov, A.N., E.N. Kashinskaya, E.P. Simonov, O.V. Hlunov, G.I. Izvekova, K.B. Andree, and M.M. Solovyev. 2019. "Variations Of The Intestinal Gut Microbiota Of Farmed Rainbow Trout, Oncorhynchus Mykiss (Walbaum), Depending On The Infection Status Of The Fish". Journal Of Applied Microbiology. Wiley. doi:10.1111/jam.14302., which has been published in final form at https://doi.org/10.1111/jam.14302. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions http://www.wileyauthors.com/self- archiving. DR. ALEKSEY PARSHUKOV (Orcid ID : 0000-0001-9917-186X) MISS ELENA KASHINSKAYA (Orcid ID : 0000-0001-8097-2333) Article type : - Original Article Variations of the intestinal gut microbiota of farmed rainbow trout, Oncorhynchus mykiss (Walbaum), depending on the infection status of the fish Article A.N. Parshukov1*¥, E.N. Kashinskaya2¥, E.P. Simonov2,3¥, O.V. Hlunov4, G.I. Izvekova5, K.B. Andree6, M.M. Solovyev2,7** 1Institute of Biology of the Karelian Research Centre of the Russian Academy of Sciences, Petrozavodsk, Russia 2Institute of Systematics and Ecology of Animals, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia 3Laboratory for Genomic Research and Biotechnology, Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk, Russia 4LLC “FishForel”, Lahdenpohja, Karelia, Russia 5Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Nekouzskii raion, Yaroslavl oblast, Russia 6IRTA-SCR, San Carlos de la Rapita, Tarragona, Spain 7Tomsk State University, Tomsk, Russia This article has been accepted for publication and undergone full peer review but has not Accepted been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record.
    [Show full text]
  • Enterolignan-Producing Phenotypes Are Associated with Increased Gut Microbial Diversity and Altered Composition in Premenopausal Women in the United States
    Published OnlineFirst December 26, 2014; DOI: 10.1158/1055-9965.EPI-14-0262 Research Article Cancer Epidemiology, Biomarkers Enterolignan-Producing Phenotypes Are & Prevention Associated with Increased Gut Microbial Diversity and Altered Composition in Premenopausal Women in the United States Meredith A.J. Hullar1, Samuel M. Lancaster1,2, Fei Li2, Elizabeth Tseng2, Karlyn Beer2, Charlotte Atkinson3, Kristiina Wah€ al€ a€4, Wade K. Copeland1, Timothy W. Randolph1, Katherine M. Newton5, and Johanna W. Lampe1,2 Abstract Background: Lignans in plant foods are metabolized by gut ysis and regression were used to model the association between bacteria to the enterolignans, enterodiol (END) and enterolac- enterolignan excretion and the GMC. Bacteria associated with tone (ENL). Enterolignans have biologic activities important to ENL production were identified using univariate analysis and the prevention of cancer and chronic diseases. We examined the ridge regression. composition of the gut microbial community (GMC) as a con- Results: After adjusting for dietary fiber intake and adiposity, tributor to human enterolignan exposure. we found a significant positive association between ENL excretion Methods: We evaluated the association between the GMC in and either the GMC (P ¼ 0.0007), or the diversity of the GMC (P ¼ stool, urinary enterolignan excretion, and diet from a 3-day food 0.01). The GMC associated with high ENL production was distinct record in 115 premenopausal (ages 40–45 years) women in the (UNIFRAC, P < 0.003, MRPP) and enriched in Moryella spp., United States. Urinary enterolignans were measured using gas Acetanaerobacterium spp., Fastidiosipila spp., and Streptobacillus spp. chromatography–mass spectroscopy. The GMC was evaluated Conclusion: Diversity and composition of the GMC are asso- using 454 pyrosequencing of the 16S rRNA gene.
    [Show full text]
  • Abstract Tracing Hydrocarbon
    ABSTRACT TRACING HYDROCARBON CONTAMINATION THROUGH HYPERALKALINE ENVIRONMENTS IN THE CALUMET REGION OF SOUTHEASTERN CHICAGO Kathryn Quesnell, MS Department of Geology and Environmental Geosciences Northern Illinois University, 2016 Melissa Lenczewski, Director The Calumet region of Southeastern Chicago was once known for industrialization, which left pollution as its legacy. Disposal of slag and other industrial wastes occurred in nearby wetlands in attempt to create areas suitable for future development. The waste creates an unpredictable, heterogeneous geology and a unique hyperalkaline environment. Upgradient to the field site is a former coking facility, where coke, creosote, and coal weather openly on the ground. Hydrocarbons weather into characteristic polycyclic aromatic hydrocarbons (PAHs), which can be used to create a fingerprint and correlate them to their original parent compound. This investigation identified PAHs present in the nearby surface and groundwaters through use of gas chromatography/mass spectrometry (GC/MS), as well as investigated the relationship between the alkaline environment and the organic contamination. PAH ratio analysis suggests that the organic contamination is not mobile in the groundwater, and instead originated from the air. 16S rDNA profiling suggests that some microbial communities are influenced more by pH, and some are influenced more by the hydrocarbon pollution. BIOLOG Ecoplates revealed that most communities have the ability to metabolize ring structures similar to the shape of PAHs. Analysis with bioinformatics using PICRUSt demonstrates that each community has microbes thought to be capable of hydrocarbon utilization. The field site, as well as nearby areas, are targets for habitat remediation and recreational development. In order for these remediation efforts to be successful, it is vital to understand the geochemistry, weathering, microbiology, and distribution of known contaminants.
    [Show full text]
  • Taxonomic and Functional Characterization of Human Gut Microbes Involved in Dietary Plant Lignan Metabolism
    Taxonomic and Functional Characterization of Human Gut Microbes Involved in Dietary Plant Lignan Metabolism Isaac M. Elkon A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science University of Washington 2015 Committee: Johanna W. Lampe Meredith A.J. Hullar Program Authorized to Offer Degree: School of Public Health © Copyright 2015 Isaac M. Elkon University of Washington Abstract Taxonomic and Functional Characterization of Human Gut Microbes Involved in Dietary Plant Lignan Metabolism Isaac M. Elkon Chair of the Supervisory Committee: Research Professor Johanna W. Lampe Department of Epidemiology Background: Dietary plant lignans, such as secoisolariciresinol diglucoside (SDG), are metabolized to the enterolignans, enterodiol (END) and enterolactone (ENL), by gut microbes. Evidence suggests that enterolignans may reduce risk of cardiovascular disease and several forms of cancer. Our aim was to characterize the microbial community involved in enterolignan production by using an in vitro batch culture system to enrich for lignan-metabolizing organisms. Methods: Stool samples from eight participants were incubated separately for ~1 week with a mineral salts media containing formate, acetate, glucose, and 6.55 µM SDG. Daily secoisolariciresinol (SECO), END, and ENL concentrations were measured using gas chromatography–mass spectrometry (GCMS). Microbial community in initial stool (Day 1) and in vitro-incubated fecal suspensions (final-day) was assessed via Illumina paired-end 16S rRNA gene amplicon and whole-metagenome shotgun sequencing. 16S rRNA gene sequences were taxonomically annotated using an in-house QIIME pipeline. Metagenomic shotgun sequences were taxonomically annotated using MetaPhlAn and functionally annotated using DIAMOND and HUMAnN. Annotation-based alpha diversity, organism abundance, and functional gene abundance were used to assess differences between Day 1 and final-day microbial community composition.
    [Show full text]
  • Weaning Piglet Gut Microbiome 3 4 D
    bioRxiv preprint doi: https://doi.org/10.1101/2020.07.20.211326; this version posted July 20, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Community composition and development of the post- 2 weaning piglet gut microbiome 3 4 D. Gaio1, Matthew Z. DeMaere1, Kay Anantanawat1, Graeme J. Eamens2, Michael Liu1, 5 Tiziana Zingali1, Linda Falconer2, Toni A. Chapman2, Steven P. Djordjevic1, Aaron E. 6 Darling1* 7 1The ithree institute, University of Technology Sydney, Sydney, NSW, Australia 8 2NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, 9 Menangle, NSW, Australia 10 *Corresponding author: Aaron E. Darling, [email protected] 11 12 Keywords: shotgun metagenomics; pig; post-weaning; gut microbiome; phylogenetic 13 diversity 14 15 ABSTRACT 16 We report on the largest metagenomic analysis of the pig gut microbiome to date. By 17 processing over 800 faecal time-series samples from 126 piglets and 42 sows, we generated 18 over 8Tbp of metagenomic shotgun sequence data. Here we describe the animal trial 19 procedures, the generation of our metagenomic dataset and the analysis of the microbial 20 community composition using a phylogenetic framework. We assess the effects of 21 intramuscular antibiotic treatment and probiotic oral treatment on the diversity of gut 22 microbial communities. We found differences between individual hosts such as breed, litter, 23 and age, to be important contributors to variation in the community composition.
    [Show full text]
  • Environmental Impact on Differential Composition of Gut Microbiota In
    microorganisms Article Environmental Impact on Differential Composition of Gut Microbiota in Indoor Chickens in Commercial Production and Outdoor, Backyard Chickens Zuzana Seidlerova, Tereza Kubasova, Marcela Faldynova, Magdalena Crhanova, Daniela Karasova, Vladimir Babak and Ivan Rychlik * Veterinary Research Institute, 62100 Brno, Czech Republic; [email protected] (Z.S.); [email protected] (T.K.); [email protected] (M.F.); [email protected] (M.C.); [email protected] (D.K.); [email protected] (V.B.) * Correspondence: [email protected]; Tel.: +420-533331201 Received: 8 April 2020; Accepted: 18 May 2020; Published: 20 May 2020 Abstract: In this study, we compared the caecal microbiota composition of egg-laying hens from commercial production that are kept indoors throughout their whole life with microbiota of hens kept outdoors. The microbiota of outdoor hens consisted of lower numbers of bacterial species than the microbiota of indoor hens. At the phylum level, microbiota of outdoor hens was enriched for Bacteroidetes (62.41 4.47% of total microbiota in outdoor hens and 52.01 6.27% in indoor ± ± hens) and Proteobacteria (9.33 4.99% in outdoor and 5.47 2.24% in indoor hens). On the other ± ± hand, Firmicutes were more abundant in the microbiota of indoor hens (33.28 5.11% in indoor ± and 20.66 4.41% in outdoor hens). Horizontally transferrable antibiotic resistance genes tetO, ± tet(32), tet(44), and tetW were also less abundant in the microbiota of outdoor hens than indoor hens. A comparison of the microbiota composition at the genus and species levels pointed toward isolates specifically adapted to the two extreme environments.
    [Show full text]
  • Abnormal Composition of Gut Microbiota Is Associated
    Zhang et al. Translational Psychiatry (2019) 9:231 https://doi.org/10.1038/s41398-019-0571-x Translational Psychiatry ARTICLE Open Access Abnormal composition of gut microbiota is associated with resilience versus susceptibility to inescapable electric stress Kai Zhang1,2, Yuko Fujita1, Lijia Chang1,YougeQu1,YaoyuPu1, Siming Wang1, Yukihiko Shirayama1,3 and Kenji Hashimoto 1 Abstract Increasing evidence indicates that abnormalities in the composition of gut microbiota might play a role in stress-related disorders. In the learned helplessness (LH) paradigm, ~60–70% rats are susceptible to LH in the face of inescapable electric stress. The role of gut microbiota in susceptibility in the LH paradigm is unknown. In this study, male rats were exposed to inescapable electric stress under the LH paradigm. The compositions of gut microbiota and short-chain fatty acids were assessed in fecal samples from control rats, non-LH (resilient) rats, and LH (susceptible) rats. Members of the order Lactobacillales were present at significantly higher levels in the susceptible rats than in control and resilient rats. At the family level, the number of Lactobacillaceae in the susceptible rats was significantly higher than in control and resilient rats. At the genus level, the numbers of Lactobacillus, Clostridium cluster III, and Anaerofustis in susceptible rats were significantly higher than in control and resilient rats. Levels of acetic acid and propionic acid in the feces of susceptible rats were lower than in those of control and resilient rats; however, the levels of lactic acid in the susceptible rats were higher than those of control and resilient rats. There was a positive correlation between lactic acid and Lactobacillus levels among these three fi 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; groups.
    [Show full text]
  • Abstract Mammalian Derived Ruminococcaceae
    ABSTRACT MAMMALIAN DERIVED RUMINOCOCCACEAE POPULATION AS MOLECULAR TARGET OF FECAL CONTAMINATION By Nilay J. Sheth Domesticated animal’s fecal material, as agricultural runoff is a contributor to decreased water quality and subsequent, human exposure to waterborne illness. Fecal contamination of water sources is currently monitored by bacteria indicators such as Escherichia coli (E. coli), enterococci, or fecal coliforms. However, these bacteria typically comprise less than 1% of the intestinal bacterial population, and may not precisely predict the human health risk associated with fecal contamination. The mammalian intestinal tract is dominated by the bacterial phylum Firmicutes and a major population is the family Ruminococcaceae. The main objective of this research was to determine if animal derived Ruminococcaceae can be used as an alternative molecular indicator target for the detection of fecal pollution in surface water. To address this objective a 16S rRNA molecular target for mammalian specific Ruminococcaceae was created using the characterized diversity of rumen gastrointestinal/fecal microbial community. The Ruminococcaceae target was amplified from the fecal DNA samples of dairy cow, pig, goat, camel, bison, and water buffalo. The target population was not amplified from horse, chicken, goose, and human sewage influent DNA samples. In natural water spiked with fresh cow fecal material; the culturable indicator E. coli was detected for four days as compared to one day post inoculation, illustrating rapid signal loss. Following rain events, this population was detected in surface water samples from Spring Brook creek (n=10) and only one sample from Fox River, indicating this creek receives animal fecal pollution. The bacterial community analysis of Spring Brook and Fox River water samples demonstrated an increased diversity in the Spring Brook samples.
    [Show full text]
  • Eukaryotic and Prokaryotic Microbiota Interactions
    microorganisms Review Eukaryotic and Prokaryotic Microbiota Interactions Aly Kodio 1,2,3, Estelle Menu 1,2 and Stéphane Ranque 1,2,* 1 Aix-Marseille Université, Instiut de Recherche pour le Développement, Assistance Publique Hôpitaux de Marseille, Service de Santé des Armées, Vecteurs et Infections TROpicales et MEditerranéennes, 13005 Marseille, France; [email protected] (A.K.); [email protected] (E.M.) 2 IHU-Méditerranée Infection, 13005 Marseille, France 3 Malaria Research and Training Center, International Centers for Excellence in Research, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako BP 1805, Mali * Correspondence: [email protected] Received: 4 November 2020; Accepted: 5 December 2020; Published: 17 December 2020 Abstract: The nature of the relationship between the communities of microorganisms making up the microbiota in and on a host body has been increasingly explored in recent years. Microorganisms, including bacteria, archaea, viruses, parasites and fungi, have often long co-evolved with their hosts. In human, the structure and diversity of microbiota vary according to the host’s immunity, diet, environment, age, physiological and metabolic status, medical practices (e.g., antibiotic treatment), climate, season and host genetics. The recent advent of next generation sequencing (NGS) technologies enhanced observational capacities and allowed for a better understanding of the relationship between distinct microorganisms within microbiota. The interaction between the host and
    [Show full text]
  • Dr Bernard Taminiau Dr Cristina Rodriguez Pr Georges Daube CLOSTRIDIA
    Clostridia in the Gut Microbiota and Their Implication in Food Allergies and Foodborne Diseases Dr Bernard Taminiau Dr Cristina Rodriguez Pr Georges Daube CLOSTRIDIA 80’s 2005 16S NGS taxonomy Cato, E.P. and Collins et al 1994 SILVA DB 2016 Stackebrandt, E 1989 82141 non redundant 30 known sp 110 k n ow n a n d unamed sp 16S Clostridium is a Cluster I (Clostridium ss) to 34 Families composite group Cluster XIX (Fusobacterium) Majority unknown species Lack of phenotypic Lack of culture availability discriminating properties Deficit in wet lab compared to sequences ULg – Faculté de Médecine Vétérinaire - FARAH 2 Microbiota - the new organ Cultivable Unknown or non cultivable ULg – Faculté de Médecine Vétérinaire - FARAH 3 Key determinants Pre-birth contact Colonization and Increasing sensitivity with bacteria tolerance building to disorder Kerr et al Crit Rev Microbiol 2014 online 19 March 2014 Microbiota and host Outside the Immune system relationship, microbiota is a key player Bile acid Obesity metabolism Behavior diabetes Thermogenesis atherosclerose Intestinal Metabolic disease gluconeogenesis Appetite Asthma Hormone autism expression Schroeder et al 2016 ULg – Faculté de Médecine Vétérinaire - FARAH 5 Infant-type microbiota and Clostridia Bacterial flora Colonisation by heterogeneous, Clostridium spp. Sterile independent of and other obligate GI tract feeding habits anaerobes Birth First few First month days Gradual Bacteria from consumption the mother of oxygen by and the aerobic environment bacteria colonize de GI (conditions tract of for a more neonates diversified flora) Jost et al., 2012 ULg – Faculté de Médecine Vétérinaire - FARAH Lopetuso et al., 2013 Elderly-type microbiota The aging process challenges the stability of microbiota and can also affect the presence of Clostridium spp.
    [Show full text]
  • SUPPLEMENTARY DATA Supplementary Table 1. Bacterial
    SUPPLEMENTARY DATA Supplementary Table 1. Bacterial genus differences between chow and HF‐feeding High-Fat Diet Chow Diet P-values High-Fat Diet Chow Diet P-values Phylum Genus Mean SD FQ (%) Mean SD FQ (%) HF vs Chow Phylum Genus Mean SD FQ (%) Mean SD FQ (%) HF vs Chow Actinobacteria Bifidobacterium 0.00 0.00 0.00 0.00 0.01 11.11 0.3428 Firmicutes Marvinbryantia 0.00 0.01 10.00 0.06 0.05 77.78 0.0031 Actinobacteria Adlercreutzia 0.04 0.04 50.00 0.01 0.02 11.11 0.0671 Firmicutes Moryella 0.00 0.00 0.00 0.10 0.08 88.89 0.0003 Actinobacteria Asaccharobacter 0.01 0.01 20.00 0.00 0.00 0.00 0.1930 Firmicutes Oribacterium 0.00 0.01 10.00 0.02 0.01 66.67 0.0083 Actinobacteria Coriobacterium 0.00 0.00 0.00 0.00 0.00 0.00 NA Firmicutes Parasporobacterium 0.00 0.00 0.00 0.05 0.06 55.56 0.0099 Actinobacteria Cryptobacterium 0.00 0.00 0.00 0.00 0.01 11.11 0.3428 Firmicutes Pseudobutyrivibrio 0.00 0.00 0.00 0.01 0.01 22.22 0.1457 Actinobacteria Enterorhabdus 0.01 0.02 20.00 0.00 0.00 0.00 0.1930 Firmicutes Robinsoniella 0.02 0.05 10.00 0.24 0.15 88.89 0.0008 Actinobacteria Olsenella 0.00 0.00 0.00 0.01 0.01 22.22 0.1457 Firmicutes Roseburia 0.77 0.53 100.00 0.64 0.57 100.00 0.4470 Actinobacteria Paraeggerthella 0.00 0.00 0.00 0.01 0.01 22.22 0.1457 Firmicutes Syntrophococcus 0.00 0.00 0.00 0.01 0.03 33.33 0.0624 Actinobacteria Corynebacterium 0.01 0.03 20.00 0.00 0.00 0.00 0.1930 Firmicutes unclassified_Lachnospiraceae 9.81 4.46 100.00 39.77 4.00 100.00 0.0000 Actinobacteria Rothia 0.03 0.07 30.00 0.00 0.01 11.11 0.3306 Firmicutes Desulfonispora 0.03
    [Show full text]