DOCSLIB.ORG

Coaggregation of Gut Bacteroides & Parabacteroides with Probiotic Lactobacillus Rhamnosus GG Samuel Schotten

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Coaggregation of Gut Bacteroides & Parabacteroides with Probiotic Lactobacillus Rhamnosus GG Samuel Schotten Eastern Michigan University DigitalCommons@EMU Senior Honors Theses Honors College 2016 Coaggregation of Gut Bacteroides & Parabacteroides with Probiotic Lactobacillus Rhamnosus GG Samuel Schotten Follow this and additional works at: http://commons.emich.edu/honors Recommended Citation Schotten, Samuel, "Coaggregation of Gut Bacteroides & Parabacteroides with Probiotic Lactobacillus Rhamnosus GG" (2016). Senior Honors Theses. 474. http://commons.emich.edu/honors/474 This Open Access Senior Honors Thesis is brought to you for free and open access by the Honors College at DigitalCommons@EMU. It has been accepted for inclusion in Senior Honors Theses by an authorized administrator of DigitalCommons@EMU. For more information, please contact lib- [email protected]. Coaggregation of Gut Bacteroides & Parabacteroides with Probiotic Lactobacillus Rhamnosus GG Abstract Coaggregation has been indicated as a key mechanism in the formation of biofilms. This research sought to characterize the interactions occurring between native gastrointestinal Bacteroides & Parabacteroides and the probiotic strain Lactobacillus rhamnosus GG (LGG) cultured in Todd Hewitt TH( ), deMan, Rogosa, and Sharpe (MRS), and Brain Heart Infusion (BHI) using in vitro coaggregation assays. In the coaggregation survey of interactions, a trend of growth medium-dependent coaggregation variability was displayed with LGG grown in TH displaying the widest spectrum of coaggregation with Bacteroides/Parabacteroides strains and narrower spectrum from the other cultures of LGG. By protease inhibition, it was confirmed that the presence of novel adhesin(s) occurs on LGG, mediating coaggregation with moderate strength to a variety of Bacteroides & Parabacteroides strains abundant in the large intestine, including selective interactions with capsule-deficient mutants of B. thetaiotaomicron VPI-5482. In the case of LGG grown in MRS, bimodal adhesin interaction with involvement of Bacteroides/Parabacteroides partners was observed. These interactions were not reversed by the addition of a variety of simple sugars, providing no support for the presence of a lectin-like adhesion on LGG, and thus the affinity of the adhesin(s) involved remains to be characterized. Degree Type Open Access Senior Honors Thesis Department Biology First Advisor Daniel Clemans Second Advisor Kristin E. Judd Keywords biofilm, microbe, adhesion, gastrointestinal, probiotic, microbiology This open access senior honors thesis is available at DigitalCommons@EMU: http://commons.emich.edu/honors/474 COAGGREGATION OF GUT BACTEROIDES & PARABACTEROIDES WITH PROBIOTIC UCTOBACJUUS RHAMNOSUSGG By Samuel Schotten A Senior Thesis Submitted to the EasternMichigan University Honors College in Panial Fulfillmentof the Requirement for Graduationwith Honors in Biology Approved al Ypsilanti, Michigan, on this date �"' \ { 'l.\,, LO�\, TABLE OF CONTENTS ABSTRACT........................................................................................................ l INTRODUCTION.............................................................................................. 2 MATERIALS & METHODS............................................................................ 8 RESULTS........................................................................................................... 15 DISCUSSION..................................................................................................... 24 APPENDICES .................................................................................................... 29 REFERENCES................................................................................................... 32 ACKNOWLEDGEMENTS I would like to thank my faculty mentor Dr. Daniel Clemans forhis valued teachings and guidance. I would like to give special thanks to all members of the lab group who contributed to the completion of this research project, including Jamal Alhabeil, Kathryn Bryant, Kasem Ghannam, Henry Hakimaki, Radhika Hulbatte, and Gregory Kruse. I would also like to thank Lucas Waare, the graduate student who mentored me during my time being introducedto the laboratory and this fieldof research. This work would not be possible without the generous provisions of Dr. Eric Martens, Dr. Nicole Koropatkin, and Nathan Pudlo of the University of Michigan School of Medicine, Department of Microbiology and Immunology, who provided us with our Bacteroides/Parabacteroides collection of strains and the isolated capsular type mutants of B. thetaiotaomicron VPI-5482. I am very gratefulfor their aid in this project. Additionally, I am gratefulto Dr. Alexander Rickard of the University of Michigan School of Public Health, Department of Epidemiology, who was frequentlyconsulted on this project. ABSTRACT Coaggregation has been indicated as a key mechanism in the fonnation of biofilms. This research sought to characterize the interactions occurring between native gastrointestinal Bacteroides & Parabacteroides and the probiotic strain Lactobacillusrhamnosus GG (LOG) cultured in Todd Hewitt (TH), deMan, Rogosa, and Sharpe (MRS), and Brain Heart Infusion (BHI) using in vitro coaggregationassays. In the coaggregationsurvey of interactions, a trend of growthmedium-dependent coaggregationvariability was displayed with LOG grown in TH displaying the widest spectrum of coaggregationwith Bacteroides/Parabacteroides strains and narrower spectrum from the other cultures of LOG. By protease inhibition, it was confinned that the presence of novel adhesin(s) occurs on LOG, mediating coaggregationwith moderate strength to a variety of Bacteroides & Parabacteroides strains abundant in the large intestine, including selective interactions with capsule-deficientmutants of B. thetaiotaomicron VPI-5482. In the case of LOG grown in MRS, bimodal adhesin interaction with involvement of BacteroidesfParabacteroides partners was observed. These interactions were not reversed by the addition of a variety of simple sugars, providing no support forthe presence of a lectin-like adhesion on LOG, and thus the affinityof the adhesin(s) involved remains to be characterized. Keywords: Gut Bacteria, Biofilm,Probiotics 1 INTRODUCTION The formationof biofilmsis a central topic to the study of microbiota. A biofilm is a community of micro-organisms attached to either a either biotic or abiotic surface (1). Alternatively,microbial cells may occur as planktonic cells, suspended in matrix; however, it is hypothesized that the formationof sessile stage microbes in biofilmformation offer adaptive advantage for survival in a diversity of environments (2). It has been observed that a unique cooperative relationship may occur among microbes in biofilmsby the transfer of "public goods" secreted into the community by constituents (3). Key to the understanding of the formationof biofilmsand the advantage reaped by involved microbes is the mechanical understanding of cell recognitionsand interactions mediating this organization. Viable mulit-species biofilmsare observed in a diversity of habitats, including abiotic and biotic surfaces. The human body as a host for microbiota holds a large diversity of microbial species which are implicated in modulation of host physiology (4). Many studies have been conducted analyzing the unique symbiotic interface that occurs between human host cells, such as those of the epithelial surfaces, and various microbial species cells, whether pathogenic, commensal, or probiotic. Additionally, many complex metabolic and immunomodulating relationships exist between native species and the human host, especially within the human gastrointestinal tract. Accordingly, a specificniche of the human microbiome of particular interest is that of the gut, or the gastrointestinal microbiota. The lumen of the human gastrointestinal tract is one of the most diverse and most populous microbial niches of the human body. The environment of the human intestine is host to approximately 300 to 500 species of bacteria, and the number of microbial cells within the gut 2 lumen outnumber all host eukaryotic cells by a ratio of 10:1 (5). The predominate phyla in this community are the Gram-positive Firmicutes and the Gram-negative Bacteroidetes (6). In the lumen, the anaerobic bacterial species, such as those of the genus Bacteroides and Bifidobacterium, dominate, while aerobes such as genera Esclzericlzia, Klebsiella,and Lactobacillus forma smaller subset (5). The constituents of this microbiota enhance carbon and energy utilization fromdigestion. Many of these anaerobes are essential fortheir role in breakdown of complex plant polysaccharides and subsequent fermentativeproduction of short­ chain fatty acids readily absorbed across the gut epithelium, and a significant energy source for the human host (7, 8). Biofilmformation within the human gastrointestinal tract and other diverse microbial ecosystems occurs through colonization and persistence, and understanding these processes has implications forthe mediation of complex intercellular relationships and signaling. Biofilm formationis derived fromthe mechanical model of the adherence of microbial cells to a living (biotic) or non-living (abiotic) polymer substrate, which in the case of the gut is the intestinal lumen surface. It is understood that the associations subsequently formed between surface-attached microbial cells and other colonizers associated with the colonizing surface occurs with the cell surfaces of adjacent cells of either the same or differentspecies. This physical integration of cells into a community
Load more

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]
  • Description of Gabonibacter Massiliensis Gen. Nov., Sp. Nov., a New Member of the Family Porphyromonadaceae Isolated from the Human Gut Microbiota
    Curr Microbiol DOI 10.1007/s00284-016-1137-2 Description of Gabonibacter massiliensis gen. nov., sp. nov., a New Member of the Family Porphyromonadaceae Isolated from the Human Gut Microbiota 1,2 1 3,4 Gae¨l Mourembou • Jaishriram Rathored • Jean Bernard Lekana-Douki • 5 1 1 Ange´lique Ndjoyi-Mbiguino • Saber Khelaifia • Catherine Robert • 1 1,6 1 Nicholas Armstrong • Didier Raoult • Pierre-Edouard Fournier Received: 9 June 2016 / Accepted: 8 September 2016 Ó Springer Science+Business Media New York 2016 Abstract The identification of human-associated bacteria Gabonibacter gen. nov. and the new species G. mas- is very important to control infectious diseases. In recent siliensis gen. nov., sp. nov. years, we diversified culture conditions in a strategy named culturomics, and isolated more than 100 new bacterial Keywords Gabonibacter massiliensis Á Taxonogenomics Á species and/or genera. Using this strategy, strain GM7, a Culturomics Á Gabon Á Gut microbiota strictly anaerobic gram-negative bacterium was recently isolated from a stool specimen of a healthy Gabonese Abbreviations patient. It is a motile coccobacillus without catalase and CSUR Collection de Souches de l’Unite´ des oxidase activities. The genome of Gabonibacter mas- Rickettsies siliensis is 3,397,022 bp long with 2880 ORFs and a G?C DSM Deutsche Sammlung von content of 42.09 %. Of the predicted genes, 2,819 are Mikroorganismen protein-coding genes, and 61 are RNAs. Strain GM7 differs MALDI-TOF Matrix-assisted laser desorption/ from the closest genera within the family Porphyromon- MS ionization time-of-flight mass adaceae both genotypically and in shape and motility.
    [Show full text]
  • Intestinal Microbiota: a Novel Target to Improve Anti-Tumor Treatment?
    Intestinal Microbiota: A Novel Target to Improve Anti-Tumor Treatment? Romain Villeger, Amélie Lopès, Guillaume Carrier, Julie Veziant, Elisabeth Billard, Nicolas Barnich, Johan Gagnière, Emilie Vazeille, Mathilde Bonnet To cite this version: Romain Villeger, Amélie Lopès, Guillaume Carrier, Julie Veziant, Elisabeth Billard, et al.. Intestinal Microbiota: A Novel Target to Improve Anti-Tumor Treatment?. International Journal of Molecular Sciences, MDPI, 2019, 20 (18), pp.4584. 10.3390/ijms20184584. hal-02518541 HAL Id: hal-02518541 https://hal.archives-ouvertes.fr/hal-02518541 Submitted on 8 Jun 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License International Journal of Molecular Sciences Review Intestinal Microbiota: A Novel Target to Improve Anti-Tumor Treatment? 1, , 1,2, 1,3 1,4,5 Romain Villéger * y , Amélie Lopès y , Guillaume Carrier , Julie Veziant , Elisabeth Billard 1 , Nicolas Barnich 1 , Johan Gagnière 1,4,5, Emilie Vazeille 1,5,6 and Mathilde Bonnet 1 1 Microbes,
    [Show full text]
  • Thi Na Utaliblat in Un Minune Talk
    THI NA UTALIBLATUS010064900B2 IN UN MINUNE TALK (12 ) United States Patent ( 10 ) Patent No. : US 10 , 064 ,900 B2 Von Maltzahn et al . ( 45 ) Date of Patent: * Sep . 4 , 2018 ( 54 ) METHODS OF POPULATING A (51 ) Int. CI. GASTROINTESTINAL TRACT A61K 35 / 741 (2015 . 01 ) A61K 9 / 00 ( 2006 .01 ) (71 ) Applicant: Seres Therapeutics, Inc. , Cambridge , (Continued ) MA (US ) (52 ) U . S . CI. CPC .. A61K 35 / 741 ( 2013 .01 ) ; A61K 9 /0053 ( 72 ) Inventors : Geoffrey Von Maltzahn , Boston , MA ( 2013. 01 ); A61K 9 /48 ( 2013 . 01 ) ; (US ) ; Matthew R . Henn , Somerville , (Continued ) MA (US ) ; David N . Cook , Brooklyn , (58 ) Field of Classification Search NY (US ) ; David Arthur Berry , None Brookline, MA (US ) ; Noubar B . See application file for complete search history . Afeyan , Lexington , MA (US ) ; Brian Goodman , Boston , MA (US ) ; ( 56 ) References Cited Mary - Jane Lombardo McKenzie , Arlington , MA (US ); Marin Vulic , U . S . PATENT DOCUMENTS Boston , MA (US ) 3 ,009 ,864 A 11/ 1961 Gordon - Aldterton et al. 3 ,228 ,838 A 1 / 1966 Rinfret (73 ) Assignee : Seres Therapeutics , Inc ., Cambridge , ( Continued ) MA (US ) FOREIGN PATENT DOCUMENTS ( * ) Notice : Subject to any disclaimer , the term of this patent is extended or adjusted under 35 CN 102131928 A 7 /2011 EA 006847 B1 4 / 2006 U .S . C . 154 (b ) by 0 days. (Continued ) This patent is subject to a terminal dis claimer. OTHER PUBLICATIONS ( 21) Appl . No. : 14 / 765 , 810 Aas, J ., Gessert, C . E ., and Bakken , J. S . ( 2003) . Recurrent Clostridium difficile colitis : case series involving 18 patients treated ( 22 ) PCT Filed : Feb . 4 , 2014 with donor stool administered via a nasogastric tube .
    [Show full text]
  • Isolation and Characterization of ISA Degrading Alkaliphilic Bacteria
    Isolation and Characterization of ISA Degrading Alkaliphilic Bacteria Zohier Salah (Researcher) A thesis submitted to the University of Huddersfield in the partial fulfilment of the requirements for the degree of Doctor of Philosophy School of Applied Science December 2017 Acknowledgment Praise be to Allah through whose mercy (and favors) all good things are accomplished Firstly, I would like to express my sincere gratitude to my main supervisor Professor Paul N. Humphreys who gave me the opportunity to work with him and for the continuous support of my PhD study and related research, for his patience, motivation, and immense knowledge. His guidance helped me in all the time of research and writing of this thesis. Also, I wish to express my appreciation to my second supervisor, Professor Andy Laws for all the assistance he offered. Without they precious support it would not be possible to conduct this research. Special thanks go to the Government of Libya for providing me with the financial support for this study. I would also like to thank all the laboratory support staff in the School of Applied Sciences, University of Huddersfield, for all the support. Sincerely appreciations also go to my family especially, my parents and my virtuous wife Zainab, my son Mohamed and the extended my family, especially my brother Mr. Ahmed Salah. Finally, but by no means least, thanks to all my colleagues in the research group who helped with experience, ideas and discussions during my studies, Dr Simon P Rout, Dr Isaac A Kyeremeh, Dr Christopher J Charles and to all who contributed in diverse ways to make my research at the University of Huddersfield a success.
    [Show full text]
  • A Distinct Contractile Injection System Found in a Majority of Adult Human Microbiomes
    bioRxiv preprint doi: https://doi.org/10.1101/865204; this version posted December 5, 2019. 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 2 A Distinct Contractile Injection System Found in a Majority of Adult Human 3 Microbiomes 4 5 6 Maria I. Rojas*1,2, Giselle S. Cavalcanti*1,2, Katelyn McNair1,3, Sean Benler1,2, Amanda 7 T. Alker1,2, Ana G. Cobián-Güemes1,2, Melissa Giluso1,3, Kyle Levi1,3, Forest Rohwer1,2,3, 8 Sinem Beyhan2,4, Robert A. Edwards1,2,3, Nicholas J. Shikuma#1,2,3,4 9 10 11 1Viral Information Institute 12 San Diego State University 13 San Diego, California 92182 USA 14 15 2Department of Biology 16 San Diego State University 17 San Diego, California 92182 USA 18 19 3Computational Science Research Center 20 San Diego State University 21 San Diego, California 92182 USA 22 23 4Department of Infectious Diseases 24 J. Craig Venter Institute 25 La Jolla, California 92037 USA 26 27 *co-first authors 28 #corresponding author 29 [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/865204; this version posted December 5, 2019. 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. 30 ABSTRACT 31 An imbalance of normal bacterial groups such as Bacteroidales within the human gut is 32 correlated with diseases like obesity. A current grand challenge in the microbiome field is 33 to identify factors produced by normal microbiome bacteria that cause these observed 34 health and disease correlations.
    [Show full text]
  • WO 2016/086209 Al June 2016 (02.06.2016) W P O P C T
    (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 2016/086209 Al June 2016 (02.06.2016) W P O P C T (51) International Patent Classification: (74) Agents: MELLO, Jill, Ann et al; Mccarter & English, A61K 35/74 (2015.01) A61P 1/00 (2006.01) LLP, 265 Franklin Street, Boston, MA 021 10 (US). A61K 35/741 (2015.01) (81) Designated States (unless otherwise indicated, for every (21) International Application Number: kind of national protection available): AE, AG, AL, AM, PCT/US20 15/062809 AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, (22) International Filing Date: DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, 25 November 2015 (25.1 1.2015) HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (25) Filing Language: English KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, (26) Publication Language: English PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, (30) Priority Data: SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 62/084,536 25 November 2014 (25. 11.2014) US TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. 62/084,537 25 November 2014 (25. 11.2014) US (84) Designated States (unless otherwise indicated, for every 62/084,540 25 November 2014 (25.
    [Show full text]
  • UNIVERSITY of CALIFORNIA Los Angeles
    UNIVERSITY OF CALIFORNIA Los Angeles Inflammatory Bowel Disease-associated Dysbiosis and Immune Gardening of the Intestinal Microbiome A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Cellular and Molecular Pathology by Jonathan Patrick Jacobs 2015 ABSTRACT OF THE DISSERTATION Inflammatory Bowel Disease-associated Dysbiosis and Immune Gardening of the Intestinal Microbiome by Jonathan Patrick Jacobs Doctor of Philosophy in Cellular and Molecular Pathology University of California, Los Angeles, 2015 Professor Jonathan Braun, Chair Inflammatory bowel disease (IBD) – comprised of Crohn’s disease (CD) and ulcerative colitis (UC) – is believed to arise from a combination of genetic susceptibility and environmental factors that trigger an inappropriate mucosal immune response to constituents of the intestinal microbiome. There is now an extensive literature demonstrating that the microbiome has profound effects on immune function and, conversely, that the immune system can shape the microbiome. I hypothesized that genetic variation in mucosal immune gardening of the intestinal microbiome can result in pro-inflammatory dysbiosis, which acts as a risk factor for overt IBD. To evaluate whether individuals at risk for IBD develop dysbiosis prior to the onset of disease, a family based study was performed to characterize the microbiome and metabolome of pediatric IBD patients and their first degree relatives. These relatives are at higher risk for dysbiosis than the general population due to shared genetic and environmental factors with the IBD proband. A ii subset of healthy relatives in this cohort had dysbiosis with fecal metabolomic profiles (metabotypes) shared with IBD patients. The effect of the transcription factor RORγt on the intestinal microbiome was then investigated as a model of how perturbation of immune gardening could result in dysbiosis.
    [Show full text]
  • Microbial and Metabolic Relationships of the Preterm Gut Microbiome in Response to Antibiotic and Dietary Interventions
    Microbial and Metabolic Relationships of the Preterm Gut Microbiome in Response to Antibiotic and Dietary Interventions by Sandi Yen A Thesis presented to The University of Guelph In partial fulfilment of requirements for the degree of Doctor of Philosophy In Molecular and Cellular Biology Guelph, Ontario, Canada © Sandi Yen, November 2019 ABSTRACT MICROBIAL AND METABOLIC RELATIONSHIPS OF THE PRETERM GUT MICROBIOME IN RESPONSE TO ANTIBIOTIC AND DIETARY INTERVENTIONS Sandi Yen Advisors: University of Guelph, 2019 Emma Allen-Vercoe Marc G. Aucoin The progression of preterm infant gut microbiome development is intricately linked with the development of the infant, such that disruptions to the microbial system can manifest as neonatal necrotizing enterocolitis (NEC) in the infant. One of the proposed aetiologies of NEC is that disease onset occurs when microbiome development is challenged by an external perturbation, such as antibiotic treatment. The research conducted in this thesis was motivated by the overarching hypothesis that infant health occurs when homeostatic microbial relationships have been established. Conversely, when microbiome development is disrupted, the preterm infant is susceptible to diseases such as NEC. Therefore, the driving hypothesis of this thesis was that external factors, such as antibiotic therapy or formula milk, impair microbial interactions such that the preterm gut microbiome no longer sustains healthy infant development, leading to NEC onset. This hypothesis was tested using fecal microbiota from two preterm infants with different antibiotic exposures while in hospital. Propagation of these preterm fecal microbiota in an in vitro continuous culture system allowed for compositional, metabonomic, culture-based annotation of the ecosystems. Longitudinal analysis of each community revealed differences in each community’s functional capacity.
    [Show full text]
  • Transcriptomic and Metagenomic Impacts of Dietary Energy of Milk Replacer in Pre- Weaned Holstein Heifers
    Transcriptomic and metagenomic impacts of dietary energy of milk replacer in pre- weaned Holstein heifers Connor Owens Thesis submitted to the faculty of the Virginia Polytechnic Institute and State University in partial fulfillment of the requirements for the degree of Master of Science In Dairy Science Rebecca Cockrum Kristy Daniels Alan Ealy May 5, 2017 Blacksburg, VA Keywords: Dairy, Calf management, Rumen microbiome, Transcriptome, Growth and development. Transcriptomic and metagenomic impacts of dietary energy of milk replacer in pre- weaned Holstein heifers Connor Owens ACADEMIC ABSTRACT The variability in calf management can change the physiological state of the calf as they are weaned or attain puberty. It is up to the producer to ensure that the calves develop properly to meet their expected needs on the farm. While there are guidelines from the NRC in place, there is a substantial range in the amount of protein and fat that a calf can be fed. This physiological state can be reflected in the proteins produced in tissues, the expression of gene regulatory pathways, or even the microbes present in the gut. The purpose of this study was to examine how an increase in dietary energy in milk replacer of pre-weaned Holstein heifers impacts the microbial profile of the rumen as well as the transcriptome in tissues related to growth and metabolism. Our hypothesis was that pre-weaned Holstein heifers on milk replacer diets with lower dietary energy will have a different rumen microbiome composition and a different transcriptome in growth related tissues. Holstein heifer calves (n = 36) were assigned randomly to 1 of 2 milk replacer diets: restricted (R; 20.9% CP, 19.8% Fat; n = 18) or enhanced (E; 28.9% CP, 26.2% Fat; n = 18).
    [Show full text]
  • Type VI Secretion Systems of Human Gut Bacteroidales Segregate Into Three Genetic Architectures, Two of Which Are Contained on Mobile Genetic Elements
    Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Coyne, Michael J., Kevin G. Roelofs, and Laurie E. Comstock. 2016. “Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements.” BMC Genomics 17 (1): 58. doi:10.1186/ s12864-016-2377-z. http://dx.doi.org/10.1186/s12864-016-2377-z. Published Version doi:10.1186/s12864-016-2377-z Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:24983903 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Coyne et al. BMC Genomics (2016) 17:58 DOI 10.1186/s12864-016-2377-z RESEARCH ARTICLE Open Access Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements Michael J. Coyne, Kevin G. Roelofs and Laurie E. Comstock* Abstract Background: Type VI secretion systems (T6SSs) are contact-dependent antagonistic systems employed by Gram negative bacteria to intoxicate other bacteria or eukaryotic cells. T6SSs were recently discovered in a few Bacteroidetes strains, thereby extending the presence of these systems beyond Proteobacteria. The present study was designed to analyze in a global nature the diversity, abundance, and properties of T6SSs in the Bacteroidales, the most predominant Gram negative bacterial order of the human gut.
    [Show full text]
  • Type VI Secretion Systems of Human Gut Bacteroidales Segregate Into Three Genetic Architectures, Two of Which Are Contained on Mobile Genetic Elements Michael J
    Coyne et al. BMC Genomics (2016) 17:58 DOI 10.1186/s12864-016-2377-z RESEARCH ARTICLE Open Access Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements Michael J. Coyne, Kevin G. Roelofs and Laurie E. Comstock* Abstract Background: Type VI secretion systems (T6SSs) are contact-dependent antagonistic systems employed by Gram negative bacteria to intoxicate other bacteria or eukaryotic cells. T6SSs were recently discovered in a few Bacteroidetes strains, thereby extending the presence of these systems beyond Proteobacteria. The present study was designed to analyze in a global nature the diversity, abundance, and properties of T6SSs in the Bacteroidales, the most predominant Gram negative bacterial order of the human gut. Results: By performing extensive bioinformatics analyses and creating hidden Markov models for Bacteroidales Tss proteins, we identified 130 T6SS loci in 205 human gut Bacteroidales genomes. Of the 13 core T6SS proteins of Proteobacteria, human gut Bacteroidales T6SS loci encode orthologs of nine, and an additional five other core proteins not present in Proteobacterial T6SSs. The Bacteroidales T6SS loci segregate into three distinct genetic architectures with extensive DNA identity between loci of a given genetic architecture. We found that divergent DNA regions of a genetic architecture encode numerous types of effector and immunity proteins and likely include new classes of these proteins. TheT6SS loci of genetic architecture 1 are contained on highly similar integrative conjugative elements (ICEs), as are the T6SS loci of genetic architecture 2, whereas the T6SS loci of genetic architecture 3 are not and are confined to Bacteroides fragilis.
    [Show full text]