Comparison of Gut Microbiota Between Adults with Autism Spectrum Disorder and Obese Adults
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WO 2015/066625 Al 7 May 2015 (07.05.2015) 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 2015/066625 Al 7 May 2015 (07.05.2015) P O P C T (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every C12Q 1/04 (2006.01) G01N 33/15 (2006.01) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, (21) International Application Number: BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, PCT/US2014/06371 1 DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (22) International Filing Date: HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, 3 November 20 14 (03 .11.20 14) KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, (25) Filing Language: English PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, (26) Publication Language: English 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. (30) Priority Data: 61/898,938 1 November 2013 (01. 11.2013) (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, (71) Applicant: WASHINGTON UNIVERSITY [US/US] GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, One Brookings Drive, St. -
Fatty Acid Diets: Regulation of Gut Microbiota Composition and Obesity and Its Related Metabolic Dysbiosis
International Journal of Molecular Sciences Review Fatty Acid Diets: Regulation of Gut Microbiota Composition and Obesity and Its Related Metabolic Dysbiosis David Johane Machate 1, Priscila Silva Figueiredo 2 , Gabriela Marcelino 2 , Rita de Cássia Avellaneda Guimarães 2,*, Priscila Aiko Hiane 2 , Danielle Bogo 2, Verônica Assalin Zorgetto Pinheiro 2, Lincoln Carlos Silva de Oliveira 3 and Arnildo Pott 1 1 Graduate Program in Biotechnology and Biodiversity in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande 79079-900, Brazil; [email protected] (D.J.M.); [email protected] (A.P.) 2 Graduate Program in Health and Development in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande 79079-900, Brazil; pri.fi[email protected] (P.S.F.); [email protected] (G.M.); [email protected] (P.A.H.); [email protected] (D.B.); [email protected] (V.A.Z.P.) 3 Chemistry Institute, Federal University of Mato Grosso do Sul, Campo Grande 79079-900, Brazil; [email protected] * Correspondence: [email protected]; Tel.: +55-67-3345-7416 Received: 9 March 2020; Accepted: 27 March 2020; Published: 8 June 2020 Abstract: Long-term high-fat dietary intake plays a crucial role in the composition of gut microbiota in animal models and human subjects, which affect directly short-chain fatty acid (SCFA) production and host health. This review aims to highlight the interplay of fatty acid (FA) intake and gut microbiota composition and its interaction with hosts in health promotion and obesity prevention and its related metabolic dysbiosis. -
Title: Gut Microbiome Profiles and Associated Metabolic Pathways in HIV-Infected Treatment-Naïve Patients Wellinton M. Do Nasci
medRxiv preprint doi: https://doi.org/10.1101/2020.12.07.20245530; this version posted December 8, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Title: Gut microbiome profiles and associated metabolic pathways in HIV-infected treatment-naïve patients Wellinton M. do Nascimento1,2, Aline Machiavelli2, Luiz G. E. Ferreira3, Luisa Cruz Silveira1, Suwellen S. D. de Azevedo4, Gonzalo Bello4, Daniel P. Smith5, Melissa P. Mezzari5, Joseph Petrosino5, Rubens Tadeu Delgado Duarte6, Carlos R. Zaráte- Bládes2§*, and Aguinaldo R. Pinto1* 1 Laboratório de Imunologia Aplicada, LIA, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Campus Universitário da Trindade, Florianópolis, SC, 88034-040, Brazil. 2 Laboratório de Imunoregulação, iREG, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Campus Universitário da Trindade, Florianópolis, SC, 88034-040, Brazil. 3 Hospital Regional Homero de Miranda Gomes, Rua Adolfo Donato da Silva, s/n, São José, SC, 88103-901, Brazil. 4 Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Av. Brasil, 4365, Rio de Janeiro, RJ, 21045-900, Brazil. 5 Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, United States. 6 Laboratório de Ecologia Molecular e Extremófilos, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Campus Universitário da Trindade, Florianópolis, SC, 88034-040, Brazil. *contributed equally to this work NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. -
Robust Taxonomic Classification of Uncharted Microbial Sequences and Bins with CAT and BAT
bioRxiv preprint doi: https://doi.org/10.1101/530188; this version posted January 24, 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 4.0 International license. Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT F.A. Bastiaan von Meijenfeldt1,†, Ksenia Arkhipova1,†, Diego D. Cambuy1, Felipe H. Coutinho2,3, Bas E. Dutilh1,2,* 1 Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, The Netherlands. 2 Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands. 3 Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. * To whom correspondence should be addressed. Tel: +31 30 253 4212; Email: [email protected]. † These authors contributed equally to this work. Present Address: [Felipe H. Couthinho], Evolutionary Genomics Group, Departamento de Produccíon y Microbiología, Universidad Miguel Hernández, Campus San Juan, San Juan, Alicante 03550, Spain. ABSTRACT Current-day metagenomics increasingly requires taxonomic classification of long DNA sequences and metagenome-assembled genomes (MAGs) of unknown microorganisms. We show that the standard best-hit approach often leads to classifications that are too specific. We present tools to classify high- quality metagenomic contigs (Contig Annotation Tool, CAT) and MAGs (Bin Annotation Tool, BAT) and thoroughly benchmark them with simulated metagenomic sequences that are classified against a reference database where related sequences are increasingly removed, thereby simulating increasingly unknown queries. We find that the query sequences are correctly classified at low taxonomic ranks if closely related organisms are present in the reference database, while classifications are made higher in the taxonomy when closely related organisms are absent, thus avoiding spurious classification specificity. -
Effect of Vertical Flow Exchange on Microbial Community Dis- Tributions in Hyporheic Zones
Article 1 by Heejung Kim and Kang-Kun Lee* Effect of vertical flow exchange on microbial community dis- tributions in hyporheic zones School of Earth and Environmental Sciences, Seoul National University, Seoul 08826, Republic of Korea; *Corresponding author, E-mail: [email protected] (Received: November 2, 2018; Revised accepted: January 6, 2019) https://doi.org/10.18814/epiiugs/2019/019001 The effect of the vertical flow direction of hyporheic flux advance of hydrodynamic modeling has improved research of hydro- on the bacterial community is examined. Vertical velocity logical exchange processes at the hyporheic zone (Cardenas and Wil- change of the hyporheic zone was examined by installing son, 2007; Fleckenstein et al., 2010; Endreny et al., 2011). Also, this a piezometer on the site, and a total of 20,242 reads were zone has plentiful micro-organisms. The hyporheic zone constituents analyzed using a pyrosequencing assay to investigate the a dynamic hotspot (ecotone) where groundwater and surface water diversity of bacterial communities. Proteobacteria (55.1%) mix (Smith et al., 2008). were dominant in the hyporheic zone, and Bacteroidetes This area constitutes a flow path along which surface water down wells into the streambed sediment and groundwater up wells in the (16.5%), Actinobacteria (7.1%) and other bacteria phylum stream, travels for some distance before eventually mixing with (Firmicutes, Cyanobacteria, Chloroflexi, Planctomycetesm groundwater returns to the stream channel (Hassan et al., 2015). Sur- and unclassified phylum OD1) were identified. Also, the face water enters the hyporheic zone when the vertical hydraulic head hyporheic zone was divided into 3 points – down welling of surface water is greater than the groundwater (down welling). -
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. -
Distinct Signatures of Gut Microbiome and Metabolites Associated with Significant Fibrosis in Non-Obese NAFLD
ARTICLE https://doi.org/10.1038/s41467-020-18754-5 OPEN Distinct signatures of gut microbiome and metabolites associated with significant fibrosis in non-obese NAFLD Giljae Lee 1,10, Hyun Ju You1,2,3,10, Jasmohan S. Bajaj 4, Sae Kyung Joo5, Junsun Yu1, Seoyeon Park1, ✉ Hyena Kang1, Jeong Hwan Park6, Jung Ho Kim6, Dong Hyeon Lee 5, Seonhwa Lee7, Won Kim 5 & ✉ GwangPyo Ko 1,3,8,9 1234567890():,; Nonalcoholic fatty liver disease (NAFLD) is associated with obesity but also found in non- obese individuals. Gut microbiome profiles of 171 Asians with biopsy-proven NAFLD and 31 non-NAFLD controls are analyzed using 16S rRNA sequencing; an independent Western cohort is used for external validation. Subjects are classified into three subgroups according to histological spectra of NAFLD or fibrosis severity. Significant alterations in microbiome diversity are observed according to fibrosis severity in non-obese, but not obese, subjects. Ruminococcaceae and Veillonellaceae are the main microbiota associated with fibrosis severity in non-obese subjects. Furthermore, stool bile acids and propionate are elevated, especially in non-obese subjects with significant fibrosis. Fibrosis-related Ruminococcaceae and Veillo- nellaceae species undergo metagenome sequencing, and four representative species are administered in three mouse NAFLD models to evaluate their effects on liver damage. This study provides the evidence for the role of the microbiome in the liver fibrosis pathogenesis, especially in non-obese subjects. 1 Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul 08826, Republic of Korea. 2 Institute of Health and Environment, Seoul National University, Seoul 08826, Republic of Korea. -
Exploring Salivary Microbiota in AIDS Patients with Different Periodontal Statuses Using 454 GS-FLX Titanium Pyrosequencing
ORIGINAL RESEARCH published: 02 July 2015 doi: 10.3389/fcimb.2015.00055 Exploring salivary microbiota in AIDS patients with different periodontal statuses using 454 GS-FLX Titanium pyrosequencing Fang Zhang 1 †, Shenghua He 2 †, Jieqi Jin 1, Guangyan Dong 1 and Hongkun Wu 3* 1 State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, Chengdu, China, 2 Public Health Clinical Center of Chengdu, Chengdu, China, 3 Department of Geriatric Dentistry, West China College of Stomatology, Sichuan University, Chengdu, China Patients with acquired immunodeficiency syndrome (AIDS) are at high risk of opportunistic infections. Oral manifestations have been associated with the level of immunosuppression, these include periodontal diseases, and understanding the microbial populations in the oral cavity is crucial for clinical management. The aim of this study was to examine the salivary bacterial diversity in patients newly admitted to the AIDS ward of the Public Health Clinical Center (China). Saliva samples were Edited by: Saleh A. Naser, collected from 15 patients with AIDS who were randomly recruited between December University of Central Florida, USA 2013 and March 2014. Extracted DNA was used as template to amplify bacterial Reviewed by: 16S rRNA. Sequencing of the amplicon library was performed using a 454 GS-FLX J. Christopher Fenno, University of Michigan, USA Titanium sequencing platform. Reads were optimized and clustered into operational Nick Stephen Jakubovics, taxonomic units for further analysis. A total of 10 bacterial phyla (106 genera) were Newcastle University, UK detected. Firmicutes, Bacteroidetes, and Proteobacteria were preponderant in the *Correspondence: salivary microbiota in AIDS patients. The pathogen, Capnocytophaga sp., and others Hongkun Wu, Department of Geriatric Dentistry, not considered pathogenic such as Neisseria elongata, Streptococcus mitis, and West China College of Stomatology, Mycoplasma salivarium but which may be opportunistic infective agents were detected. -
1 1 Children Developing Celiac Disease Have a Distinct And
bioRxiv preprint doi: https://doi.org/10.1101/2020.02.29.971242; this version posted March 3, 2020. 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 Children Developing Celiac Disease Have a Distinct and Proinflammatory Gut 3 Microbiota in the First 5 Years of Life 4 5 Qian Huang1, Yi Yang2, Vladimir Tolstikov3, Michael A. Kiebish3, Jonas F 6 Ludvigsson4,5, Noah W. Palm2, Johnny Ludvigsson6, Emrah Altindis1 7 8 9 Affiliations: 10 1 Boston College Biology Department, Chestnut Hill, MA 02467, USA 11 2 Department of Immunobiology, Yale University School of Medicine, New Haven, CT 12 06510, USA. 13 14 3 BERG, LLC, Framingham, MA, USA. 15 16 4 Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17 Stockholm, Sweden 18 19 5 Department of Paediatrics, Örebro University Hospital, Sweden 20 6 Crown Princess Victoria's Children's Hospital, Region Östergötland, Division of 21 Pediatrics, Linköping University, Linköping, SE 58185, Sweden. 22 23 24 25 26 27 Correspondence to: Emrah Altindis, Boston College Biology Department, Higgins Hall, 28 140 Commonwealth Avenue Chestnut Hill, MA 02467. E-mail: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.02.29.971242; this version posted March 3, 2020. 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. 29 ABSTRACT 30 Objective: Celiac disease (CD) is an immune-mediated disease characterized by small intestinal 31 inflammation. -
Diversity and Composition of the Skin, Blood and Gut Microbiome in Rosacea—A Systematic Review of the Literature
microorganisms Review Diversity and Composition of the Skin, Blood and Gut Microbiome in Rosacea—A Systematic Review of the Literature Klaudia Tutka, Magdalena Zychowska˙ and Adam Reich * Department of Dermatology, Institute of Medical Sciences, Medical College of Rzeszow University, 35-055 Rzeszow, Poland; [email protected] (K.T.); [email protected] (M.Z.)˙ * Correspondence: [email protected]; Tel.: +48-605076722 Received: 30 August 2020; Accepted: 6 November 2020; Published: 8 November 2020 Abstract: Rosacea is a chronic inflammatory skin disorder of a not fully understood pathophysiology. Microbial factors, although not precisely characterized, are speculated to contribute to the development of the condition. The aim of the current review was to summarize the rosacea-associated alterations in the skin, blood, and gut microbiome, investigated using culture-independent, metagenomic techniques. A systematic review of the PubMed, Web of Science, and Scopus databases was performed, according to PRISMA (preferred reporting items for systematic review and meta-analyses) guidelines. Nine out of 185 papers were eligible for analysis. Skin microbiome was investigated in six studies, and in a total number of 115 rosacea patients. Blood microbiome was the subject of one piece of research, conducted in 10 patients with rosacea, and gut microbiome was studied in two papers, and in a total of 23 rosacea subjects. Although all of the studies showed significant alterations in the composition of the skin, blood, or gut microbiome in rosacea, the results were highly inconsistent, or even, in some cases, contradictory. Major limitations included the low number of participants, and different study populations (mainly Asians). Further studies are needed in order to reliably analyze the composition of microbiota in rosacea, and the potential application of microbiome modifications for the treatment of this dermatosis. -
Supplementary Figure Legends for Rands Et Al. 2019
Supplementary Figure legends for Rands et al. 2019 Figure S1: Display of all 485 prophage genome maps predicted from Gram-Negative Firmicutes. Each horizontal line corresponds to an individual prophage shown to scale and color-coded for annotated phage genes according to the key displayed in the right- side Box. The left vertical Bar indicates the Bacterial host in a colour code. Figure S2: Projection of virome sequences from 183 human stool samples on A. Acidaminococcus intestini RYC-MR95, and B. Veillonella parvula UTDB1-3. The first panel shows the read coverage (Y-axis) across the complete Bacterial genome sequence (X-axis; with bp coordinates). Predicted prophage regions are marked with red triangles and magnified in the suBsequent panels. Virome reads projected outside of prophage prediction are listed in Table S4. Figure S3: The same display of virome sequences projected onto Bacterial genomes as in Figure S2, But for two different Negativicute species: A. Dialister Marseille, and B. Negativicoccus massiliensis. For non-phage peak annotations, see Table S4. Figure S4: Gene flanking analysis for the lysis module from all prophages predicted in all the different Bacterial clades (Table S2), a total of 3,462 prophages. The lysis module is generally located next to the tail module in Firmicute prophages, But adjacent to the packaging (terminase) module in Escherichia phages. 1 Figure S5: Candidate Mu-like prophage in the Negativicute Propionispora vibrioides. Phage-related genes (arrows indicate transcription direction) are coloured and show characteristics of Mu-like genome organization. Figure S6: The genome maps of Negativicute prophages harbouring candidate antiBiotic resistance genes MBL (top three Veillonella prophages) and tet(32) (bottom Selenomonas prophage remnant); excludes the ACI-1 prophage harbouring example characterised previously (Rands et al., 2018). -
Phylogenomic Analysis Supports the Ancestral Presence of LPS-Outer Membranes in the Firmicutes
Phylogenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes. Luisa Cs Antunes, Daniel Poppleton, Andreas Klingl, Alexis Criscuolo, Bruno Dupuy, Céline Brochier-Armanet, Christophe Beloin, Simonetta Gribaldo To cite this version: Luisa Cs Antunes, Daniel Poppleton, Andreas Klingl, Alexis Criscuolo, Bruno Dupuy, et al.. Phy- logenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes.. eLife, eLife Sciences Publication, 2016, 5, pp.e14589. 10.7554/eLife.14589.020. pasteur-01362343 HAL Id: pasteur-01362343 https://hal-pasteur.archives-ouvertes.fr/pasteur-01362343 Submitted on 8 Sep 2016 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 RESEARCH ARTICLE Phylogenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes Luisa CS Antunes1†, Daniel Poppleton1†, Andreas Klingl2, Alexis Criscuolo3, Bruno Dupuy4, Ce´ line Brochier-Armanet5, Christophe Beloin6, Simonetta Gribaldo1* 1Unite´ de