Microbiota-Directed Fibre Activates Both Targeted and Secondary
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Pinpointing the Origin of Mitochondria Zhang Wang Hanchuan, Hubei
Pinpointing the origin of mitochondria Zhang Wang Hanchuan, Hubei, China B.S., Wuhan University, 2009 A Dissertation presented to the Graduate Faculty of the University of Virginia in Candidacy for the Degree of Doctor of Philosophy Department of Biology University of Virginia August, 2014 ii Abstract The explosive growth of genomic data presents both opportunities and challenges for the study of evolutionary biology, ecology and diversity. Genome-scale phylogenetic analysis (known as phylogenomics) has demonstrated its power in resolving the evolutionary tree of life and deciphering various fascinating questions regarding the origin and evolution of earth’s contemporary organisms. One of the most fundamental events in the earth’s history of life regards the origin of mitochondria. Overwhelming evidence supports the endosymbiotic theory that mitochondria originated once from a free-living α-proteobacterium that was engulfed by its host probably 2 billion years ago. However, its exact position in the tree of life remains highly debated. In particular, systematic errors including sparse taxonomic sampling, high evolutionary rate and sequence composition bias have long plagued the mitochondrial phylogenetics. This dissertation employs an integrated phylogenomic approach toward pinpointing the origin of mitochondria. By strategically sequencing 18 phylogenetically novel α-proteobacterial genomes, using a set of “well-behaved” phylogenetic markers with lower evolutionary rates and less composition bias, and applying more realistic phylogenetic models that better account for the systematic errors, the presented phylogenomic study for the first time placed the mitochondria unequivocally within the Rickettsiales order of α- proteobacteria, as a sister clade to the Rickettsiaceae and Anaplasmataceae families, all subtended by the Holosporaceae family. -
16S Rdna Full-Length Assembly Sequencing Technology Analysis of Intestinal Microbiome in Polycystic Ovary Syndrome
ORIGINAL RESEARCH published: 10 May 2021 doi: 10.3389/fcimb.2021.634981 16S rDNA Full-Length Assembly Sequencing Technology Analysis of Intestinal Microbiome in Polycystic Ovary Syndrome Sitong Dong 1, Jiao jiao 1, Shuangshuo Jia 2, Gaoyu Li 1, Wei Zhang 1, Kai Yang 3, Zhen Wang 3, Chao Liu 4,DaLi1 and Xiuxia Wang 1* Edited by: 1 Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, China, 2 Department of 3 Tao Lin, Orthopedic Surgery, Shengjing Hospital of China Medical University, Shenyang, China, Department of Research and 4 Baylor College of Medicine, Development, Germountx Company, Beijing, China, Department of Biological Information, Kangwei Medical Analysis United States Laboratory, Shenyang, China Reviewed by: Barbara Obermayer-Pietsch, Objective: To study the characteristics and relationship of the gut microbiota in patients Medical University of Graz, Austria with polycystic ovary syndrome (PCOS). Julio Plaza-Diaz, Children’s Hospital of Eastern Ontario Method: We recruited 45 patients with PCOS and 37 healthy women from the (CHEO), Canada Alberto Sola-Leyva, Reproductive Department of Shengjing Hospital. We recorded their clinical indexes, University of Granada, Spain and sequenced their fecal samples by 16S rDNA full-length assembly sequencing Yanli Pang, technology (16S-FAST). Peking University Third Hospital, China Result: We found decreased a diversity and different abundances of a series of microbial *Correspondence: species in patients with PCOS compared to healthy controls. We found LH and AMH were Xiuxia Wang fi [email protected] signi cantly increased in PCOS with Prevotella enterotype when compared to control women with Prevotella enterotype, while glucose and lipid metabolism level remained no Specialty section: significant difference, and situations were opposite in PCOS and control women with This article was submitted to Bacteroides enterotype. -
Doctoral Dissertation Template
UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE METAGENOMIC INSIGHTS INTO MICROBIAL COMMUNITY RESPONSES TO LONG-TERM ELEVATED CO2 A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By QICHAO TU Norman, Oklahoma 2014 METAGENOMIC INSIGHTS INTO MICROBIAL COMMUNITY RESPONSES TO LONG-TERM ELEVATED CO2 A DISSERTATION APPROVED FOR THE DEPARTMENT OF MICROBIOLOGY AND PLANT BIOLOGY BY ______________________________ Dr. Jizhong Zhou, Chair ______________________________ Dr. Meijun Zhu ______________________________ Dr. Fengxia (Felicia) Qi ______________________________ Dr. Michael McInerney ______________________________ Dr. Bradley Stevenson © Copyright by QICHAO TU 2014 All Rights Reserved. Acknowledgements At this special moment approaching the last stage for this degree, I would like to express my gratitude to all the people who encouraged me and helped me out through the past years. Dr. Jizhong Zhou, my advisor, is no doubt the most influential and helpful person in pursuing my academic goals. In addition to continuous financial support for the past six years, he is the person who led me into the field of environmental microbiology, from a background of bioinformatics and plant molecular biology. I really appreciated the vast training I received from the many interesting projects I got involved in, without which I would hardly develop my broad experienced background from pure culture microbial genomics to complex metagenomics. Dr. Zhili He, who played a role as my second advisor, is also the person I would like to thank most. Without his help, I could be still struggling working on those manuscripts lying in my hard drive. I definitely learned a lot from him in organizing massed results into logical scientific work—skills that will benefit me for life. -
Résurrection Du Passé À L'aide De Modèles Hétérogènes D'évolution Des Séquences Protéiques
Résurrection du passé à l’aide de modèles hétérogènes d’évolution des séquences protéiques Mathieu Groussin To cite this version: Mathieu Groussin. Résurrection du passé à l’aide de modèles hétérogènes d’évolution des séquences protéiques. Biologie moléculaire. Université Claude Bernard - Lyon I, 2013. Français. NNT : 2013LYO10201. tel-01160535 HAL Id: tel-01160535 https://tel.archives-ouvertes.fr/tel-01160535 Submitted on 5 Jun 2015 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. No 201-2013 Année 2013 These` de l’universitedelyon´ Présentée devant L’UNIVERSITÉ CLAUDE BERNARD LYON 1 pour l’obtention du Diplomeˆ de doctorat (arrêté du 7 août 2006) soutenue publiquement le 8 novembre 2013 par Mathieu Groussin Résurrection du passé à l’aide de modèles hétérogènes d’évolution des séquences protéiques. Directeur de thèse : Manolo Gouy Jury : Céline Brochier-Armanet Examinateur - Président Laurent Duret Examinateur Nicolas Galtier Rapporteur Olivier Gascuel Rapporteur Manolo Gouy Directeur de thèse Dominique Madern Examinateur Hervé Philippe Examinateur 2 UNIVERSITE CLAUDE BERNARD - LYON 1 Président de l’Université M. François-Noël GILLY Vice-président du Conseil d’Administration M. le Professeur Hamda BEN HADID Vice-président du Conseil des Etudes et de la Vie Universitaire M. -
Shotgun Metagenomics of 361 Elderly Women Reveals Gut Microbiome
bioRxiv preprint doi: https://doi.org/10.1101/679985; this version posted June 23, 2019. 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-NC-ND 4.0 International license. Shotgun Metagenomics of 361 elderly women reveals gut microbiome change in bone mass loss Qi Wang1,2,3,4, *, Hui Zhao1,2,3,4, *, Qiang Sun2,5, *, Xiaoping Li3,4, *, Juanjuan Chen3,4, Zhefeng Wang6, Yanmei Ju2,3,4, Zhuye Jie3,4, Ruijin Guo3,4,7,8, Yuhu Liang2, Xiaohuan Sun3,4, Haotian Zheng3,4, Tao Zhang3,4, Liang Xiao3,4, Xun Xu3,4, Huanming Yang3,9, Songlin Peng6, †, Huijue Jia3,4,7,8, †. 1. School of Future Technology, University of Chinese Academy of Sciences, Beijing, 101408, China. 2. BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; 3. BGI-Shenzhen, Shenzhen 518083, China; 4. China National Genebank, Shenzhen 518120, China; 5. Department of Statistical Sciences, University of Toronto, Toronto, Canada; 6. Department of Spine Surgery, Shenzhen People's Hospital, Ji Nan University Second College of Medicine, 518020, Shenzhen, China. 7. Macau University of Science and Technology, Taipa, Macau 999078, China; 8. Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China; 9. James D. Watson Institute of Genome Sciences, 310058 Hangzhou, China; * These authors have contributed equally to this study †Corresponding authors: S.P., [email protected]; H.J., [email protected]; bioRxiv preprint doi: https://doi.org/10.1101/679985; this version posted June 23, 2019. -
Multi-Scale Characterization of Symbiont Diversity in the Pea Aphid
Guyomar et al. Microbiome (2018) 6:181 https://doi.org/10.1186/s40168-018-0562-9 RESEARCH Open Access Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches Cervin Guyomar1,2, Fabrice Legeai1,2, Emmanuelle Jousselin3, Christophe Mougel1, Claire Lemaitre2 and Jean-Christophe Simon1* Abstract Background: Most metazoans are involved in durable relationships with microbes which can take several forms, from mutualism to parasitism. The advances of NGS technologies and bioinformatics tools have opened opportunities to shed light on the diversity of microbial communities and to give some insights into the functions they perform in a broad array of hosts. The pea aphid is a model system for the study of insect-bacteria symbiosis. It is organized in a complex of biotypes, each adapted to specific host plants. It harbors both an obligatory symbiont supplying key nutrients and several facultative symbionts bringing additional functions to the host, such as protection against biotic and abiotic stresses. However, little is known on how the symbiont genomic diversity is structured at different scales: across host biotypes, among individuals of the same biotype, or within individual aphids, which limits our understanding on how these multi-partner symbioses evolve and interact. Results: We present a framework well adapted to the study of genomic diversity and evolutionary dynamics of the pea aphid holobiont from metagenomic read sets, based on mapping to reference genomes and whole genome variant calling. Our results revealed that the pea aphid microbiota is dominated by a few heritable bacterial symbionts reported in earlier works, with no discovery of new microbial associates. -
A Metagenomic Study of the Oral and Gut Microbiome in Crohn’S Disease Shijia Hu1* , Eileen Png2, Michelle Gowans3, David E
Hu et al. Gut Pathog (2021) 13:13 https://doi.org/10.1186/s13099-021-00409-5 Gut Pathogens RESEARCH Open Access Ectopic gut colonization: a metagenomic study of the oral and gut microbiome in Crohn’s disease Shijia Hu1* , Eileen Png2, Michelle Gowans3, David E. H. Ong3, Paola Florez de Sessions2, Jie Song2 and Niranjan Nagarajan2,4 Abstract Background: This study aims to characterize, the gut and oral microbiome in Asian subjects with Crohn’s disease (CD) using whole genome shotgun sequencing, thereby allowing for strain-level comparison. Methods: A case–control study with age, sex and ethnicity matched healthy controls was conducted. CD subjects were limited to well-controlled patients without oral manifestations. Fecal and saliva samples were collected for char- acterization of gut and oral microbiome respectively. Microbial DNA were extracted, libraries prepared and sequenced reads profled. Taxonomic diversity, taxonomic association, strain typing and microbial gene pathway analyses were conducted. Results: The study recruited 25 subjects with CD and 25 healthy controls. The oral microbe Streptococcus salivarius was found to be enriched and of concordant strains in the gut and oral microbiome of Crohn’s disease subjects. This was more likely in CD subjects with higher Crohn’s Disease Activity Index (184.3 2.9 vs 67.1 82.5, p 0.012) and active disease status (Diarrhoea/abdominal pain/blood-in-stool/fever and fatigue)± (p 0.016).± Gut species= found to be signifcantly depleted in CD compared to control (Relative abundance: Median[Range])= include: Faecalibacterium prausnitzii (0.03[0.00–4.56] vs 13.69[5.32–18.71], p 0.010), Roseburia inulinivorans (0.00[0.00–0.03] vs 0.21[0.01–0.53], p 0.010) and Alistipes senegalensis (0.00[0.00–0.00]= vs 0.00[0.00–0.02], p 0.029). -
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. -
Oat Aphid, Rhopalosiphum Padi
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by University of Dundee Online Publications University of Dundee The price of protection Leybourne, Daniel; Bos, Jorunn; Valentine, Tracy A.; Karley, Alison Published in: Insect Science DOI: 10.1111/1744-7917.12606 Publication date: 2020 Document Version Publisher's PDF, also known as Version of record Link to publication in Discovery Research Portal Citation for published version (APA): Leybourne, D., Bos, J., Valentine, T. A., & Karley, A. (2020). The price of protection: a defensive endosymbiont impairs nymph growth in the bird cherryoat aphid, Rhopalosiphum padi. Insect Science, 69-85. https://doi.org/10.1111/1744-7917.12606 General rights Copyright and moral rights for the publications made accessible in Discovery Research Portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from Discovery Research Portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain. • You may freely distribute the URL identifying the publication in the public portal. Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Download date: 24. Dec. 2019 Insect Science (2020) 27, 69–85, DOI 10.1111/1744-7917.12606 ORIGINAL ARTICLE The price of protection: a defensive endosymbiont impairs nymph growth in the bird cherry-oat aphid, Rhopalosiphum padi Daniel J. -
Dysbiosis of Small Intestinal Microbiota in Liver Cirrhosis and Its
www.nature.com/scientificreports OPEN Dysbiosis of small intestinal microbiota in liver cirrhosis and its association with etiology Received: 31 May 2016 Yanfei Chen1, Feng Ji2, Jing Guo1, Ding Shi1, Daiqiong Fang1 & Lanjuan Li1 Accepted: 22 August 2016 Cirrhosis-associated duodenal dysbiosis is not yet clearly defined. In this research, duodenal Published: 30 September 2016 mucosal microbiota was analyzed in 30 cirrhotic patients and 28 healthy controls using 16S rRNA gene pyrosequencing methods. The principal coordinate analysis revealed that cirrhotic patients were colonized by remarkable different duodenal mucosal microbiota in comparison with controls. At the genus level, Veillonella, Megasphaera, Dialister, Atopobium, and Prevotella were found overrepresented in cirrhotic duodenum. And the duodenal microbiota of healthy controls was enriched with Neisseria, Haemophilus, and SR1 genera incertae sedis. On the other hand, based on predicted metagenomes analyzed, gene pathways related to nutrient absorption (e.g. sugar and amino acid metabolism) were highly abundant in cirrhosis duodenal microbiota, and functional modules involved in bacterial proliferation and colonization (e.g. bacterial motility proteins and secretion system) were overrepresented in controls. When considering the etiology of cirrhosis, two operational taxonomic units (OTUs), OTU-23 (Neisseria) and OTU-36 (Gemella), were found discriminative between hepatitis- B-virus related cirrhosis and primary biliary cirrhosis. The results suggest that the structure of duodenal mucosa microbiota in cirrhotic patients is dramatically different from healthy controls. The duodenum dysbiosis might be related to alterations of oral microbiota and changes in duodenal micro- environment. Gut microbiota and bacterial translocation (BT) play an important role in the pathogenesis of complications of cirrhosis1. -
Mai Muun Muntant Un an to the Man Uniti
MAIMUUN MUNTANTUS009855303B2 UN AN TO THEMAN UNITI (12 ) United States Patent ( 10 ) Patent No. : US 9 , 855 ,303 B2 McKenzie et al. (45 ) Date of Patent: * Jan . 2 , 2018 ( 54 ) COMPOSITIONS AND METHODS (58 ) Field of Classification Search ??? . A61K 35 / 742 (71 ) Applicant : SERES THERAPEUTICS , INC . , See application file for complete search history . Cambridge, MA (US ) (72 ) Inventors : Gregory McKenzie , Arlington , MA ( 56 ) References Cited (US ) ; Mary - Jane Lombardo McKenzie , Arlington , MA (US ) ; David U . S . PATENT DOCUMENTS N . Cook , Brooklyn , NY (US ) ; Marin 3 ,009 , 864 A 11 / 1961 Gordon - Aldterton et al. Vulic , Boston , MA (US ) ; Geoffrey von 3 ,228 , 838 A 1 / 1966 Rinfret Maltzahn , Boston , MA (US ) ; Brian 3 ,608 ,030 A 9 / 1971 Tint Goodman , Boston , MA (US ) ; John 4 ,077 , 227 A 3 / 1978 Larson Grant Aunins , Doylestown , PA (US ) ; 4 , 205 , 132 A 5 / 1980 Sandine Matthew R . Henn , Somerville , MA 4 ,655 ,047 A 4 / 1987 Temple (US ) ; David Arthur Berry , Brookline , 4 ,689 , 226 A 8 / 1987 Nurmi MA (US ) ; Jonathan Winkler , Boston , 4 ,839 , 281 A 6 / 1989 Gorbach et al . 5 , 196 , 205 A 3 / 1993 Borody MA (US ) 5 , 425 , 951 A 6 / 1995 Goodrich 5 ,436 ,002 A 7 / 1995 Payne ( 73 ) Assignee : Seres Therapeutics , Inc ., Cambridge , 5 ,443 ,826 A 8 / 1995 Borody MA (US ) 5 , 599 , 795 A 2 / 1997 McCann 5 ,648 ,206 A 7 / 1997 Goodrich ( * ) Notice : Subject to any disclaimer , the term of this 5 , 951 , 977 A 9 / 1999 Nisbet et al. patent is extended or adjusted under 35 5 , 965 , 128 A 10 / 1999 Doyle et al . -
Integrating Taxonomic, Functional, and Strain-Level Profiling of Diverse
TOOLS AND RESOURCES Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 Francesco Beghini1†, Lauren J McIver2†, Aitor Blanco-Mı´guez1, Leonard Dubois1, Francesco Asnicar1, Sagun Maharjan2,3, Ana Mailyan2,3, Paolo Manghi1, Matthias Scholz4, Andrew Maltez Thomas1, Mireia Valles-Colomer1, George Weingart2,3, Yancong Zhang2,3, Moreno Zolfo1, Curtis Huttenhower2,3*, Eric A Franzosa2,3*, Nicola Segata1,5* 1Department CIBIO, University of Trento, Trento, Italy; 2Harvard T.H. Chan School of Public Health, Boston, United States; 3The Broad Institute of MIT and Harvard, Cambridge, United States; 4Department of Food Quality and Nutrition, Research and Innovation Center, Edmund Mach Foundation, San Michele all’Adige, Italy; 5IEO, European Institute of Oncology IRCCS, Milan, Italy Abstract Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. Opportunities for improvement continue to accelerate, with greater access to multi-omics, microbial reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set of integrated, improved methods for taxonomic, strain-level, functional, and *For correspondence: phylogenetic profiling of metagenomes newly developed to build on the largest set of reference [email protected] (CH); sequences now available. Compared to current alternatives, MetaPhlAn 3 increases the accuracy of [email protected] (EAF); taxonomic profiling, and HUMAnN 3 improves that of functional potential and activity. These [email protected] (NS) methods detected novel disease-microbiome links in applications to CRC (1262 metagenomes) and †These authors contributed IBD (1635 metagenomes and 817 metatranscriptomes).