Akkermansia Muciniphila: Key Player in Metabolic and Gastrointestinal Disorders
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The Influence of Probiotics on the Firmicutes/Bacteroidetes Ratio In
microorganisms Review The Influence of Probiotics on the Firmicutes/Bacteroidetes Ratio in the Treatment of Obesity and Inflammatory Bowel disease Spase Stojanov 1,2, Aleš Berlec 1,2 and Borut Štrukelj 1,2,* 1 Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia; [email protected] (S.S.); [email protected] (A.B.) 2 Department of Biotechnology, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia * Correspondence: borut.strukelj@ffa.uni-lj.si Received: 16 September 2020; Accepted: 31 October 2020; Published: 1 November 2020 Abstract: The two most important bacterial phyla in the gastrointestinal tract, Firmicutes and Bacteroidetes, have gained much attention in recent years. The Firmicutes/Bacteroidetes (F/B) ratio is widely accepted to have an important influence in maintaining normal intestinal homeostasis. Increased or decreased F/B ratio is regarded as dysbiosis, whereby the former is usually observed with obesity, and the latter with inflammatory bowel disease (IBD). Probiotics as live microorganisms can confer health benefits to the host when administered in adequate amounts. There is considerable evidence of their nutritional and immunosuppressive properties including reports that elucidate the association of probiotics with the F/B ratio, obesity, and IBD. Orally administered probiotics can contribute to the restoration of dysbiotic microbiota and to the prevention of obesity or IBD. However, as the effects of different probiotics on the F/B ratio differ, selecting the appropriate species or mixture is crucial. The most commonly tested probiotics for modifying the F/B ratio and treating obesity and IBD are from the genus Lactobacillus. In this paper, we review the effects of probiotics on the F/B ratio that lead to weight loss or immunosuppression. -
The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service. -
Gastrointestinal Status and Microbiota Shaping in Amyotrophic Lateral Sclerosis: a New Frontier for Targeting?
8 Gastrointestinal Status and Microbiota Shaping in Amyotrophic Lateral Sclerosis: A New Frontier for Targeting? Letizia Mazzini1 • Fabiola De Marchi1 • Elena Niccolai2 • Jessica Mandrioli3, Amedeo Amedei2 1ALS Centre, Department of Neurology, Maggiore della Carità Hospital, University of Piemonte Orientale, Novara, Italy; 2Department of Experimental and clinical Medicine, University of Florence, Firenze, Italy; 3Department of Biomedical, Metabolic and Neural Science, University of Modena and Reggio Emilia, Modena, Italy Author for correspondence: Letizia Mazzini, ALS Centre, Department of Neurology, Maggiore della Carità Hospital, University of Piemonte Orientale, Novara, Italy. Email: [email protected] Doi: https://doi.org/10.36255/exonpublications.amyotrophiclateralsclerosis. microbiota.2021 Abstract: Amyotrophic lateral sclerosis (ALS) is a rare and severe neurodegenera- tive disease affecting the upper and lower motor neurons, causing diffuse muscle paralysis. Etiology and pathogenesis remain largely unclear, but several environ- mental, genetic, and molecular factors are thought to be involved in the disease process. Emerging data identify a relationship between gut microbiota dysbiosis and neurodegenerative diseases, such as Parkinson’s disease, Alzheimer’s disease, and ALS. In these disorders, neuroinflammation is being increasingly recognized as a driver for disease onset and progression. Gut bacteria play a crucial role in In: Amyotrophic Lateral Sclerosis. Araki T (Editor), Exon Publications, Brisbane, Australia. ISBN: -
Exploring Antibiotic Susceptibility, Resistome and Mobilome Structure of Planctomycetes from Gemmataceae Family
sustainability Article Exploring Antibiotic Susceptibility, Resistome and Mobilome Structure of Planctomycetes from Gemmataceae Family Anastasia A. Ivanova *, Kirill K. Miroshnikov and Igor Y. Oshkin Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, 119071 Moscow, Russia; [email protected] (K.K.M.); [email protected] (I.Y.O.) * Correspondence: [email protected] Abstract: The family Gemmataceae accomodates aerobic, chemoorganotrophic planctomycetes with large genome sizes, is mostly distributed in freshwater and terrestrial environments. However, these bacteria have recently also been found in locations relevant to human health. Since the antimi- crobial resistance genes (AMR) from environmental resistome have the potential to be transferred to pathogens, it is essential to explore the resistant capabilities of environmental bacteria. In this study, the reconstruction of in silico resistome was performed for all nine available gemmata genomes. Furthermore, the genome of the newly isolated yet-undescribed strain G18 was sequenced and added to all analyses steps. Selected genomes were screened for the presence of mobile genetic elements. The flanking location of mobilizable genomic milieu around the AMR genes was of particular in- terest since such colocalization may appear to promote the horizontal gene transfer (HGT) events. Moreover the antibiotic susceptibility profile of six phylogenetically distinct strains of Gemmataceae planctomycetes was determined. Citation: Ivanova, A.A.; Keywords: planctomycetes; Gemmataceae; antibiotic resistance profile; resistome; mobilome Miroshnikov, K.K.; Oshkin, I.Y. Exploring Antibiotic Susceptibility, Resistome and Mobilome Structure of Planctomycetes from Gemmataceae 1. Introduction Family. Sustainability 2021, 13, 5031. Several decades ago humanity faced the global issue of growing antibiotic resistance https://doi.org/10.3390/su13095031 of bacterial pathogens in clinic [1–5]. -
Expanding the Chlamydiae Tree
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 2040 Expanding the Chlamydiae tree Insights into genome diversity and evolution JENNAH E. DHARAMSHI ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6214 ISBN 978-91-513-1203-3 UPPSALA urn:nbn:se:uu:diva-439996 2021 Dissertation presented at Uppsala University to be publicly examined in A1:111a, Biomedical Centre (BMC), Husargatan 3, Uppsala, Tuesday, 8 June 2021 at 13:15 for the degree of Doctor of Philosophy. The examination will be conducted in English. Faculty examiner: Prof. Dr. Alexander Probst (Faculty of Chemistry, University of Duisburg-Essen). Abstract Dharamshi, J. E. 2021. Expanding the Chlamydiae tree. Insights into genome diversity and evolution. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 2040. 87 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-513-1203-3. Chlamydiae is a phylum of obligate intracellular bacteria. They have a conserved lifecycle and infect eukaryotic hosts, ranging from animals to amoeba. Chlamydiae includes pathogens, and is well-studied from a medical perspective. However, the vast majority of chlamydiae diversity exists in environmental samples as part of the uncultivated microbial majority. Exploration of microbial diversity in anoxic deep marine sediments revealed diverse chlamydiae with high relative abundances. Using genome-resolved metagenomics various marine sediment chlamydiae genomes were obtained, which significantly expanded genomic sampling of Chlamydiae diversity. These genomes formed several new clades in phylogenomic analyses, and included Chlamydiaceae relatives. Despite endosymbiosis-associated genomic features, hosts were not identified, suggesting chlamydiae with alternate lifestyles. Genomic investigation of Anoxychlamydiales, newly described here, uncovered genes for hydrogen metabolism and anaerobiosis, suggesting they engage in syntrophic interactions. -
Microbial Life Under Ice: Metagenome Diversity and in Situ Activity Of
bioRxiv preprint doi: https://doi.org/10.1101/324970; this version posted May 17, 2018. 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. Microbial life under ice: metagenome diversity and in situ activity of Verrucomicrobia in seasonally ice-covered lakes Patricia Tran1,2, Arthi Ramachandran1, Ola Khawasik1, Beatrix E. Beisner2,3, Milla Rautio2,4, Yannick Huot,2,5, David A. Walsh1,2 1 Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montreal, Quebec, H4B 1R6, Canada 2 Groupe de recherche interuniversitaire en limnologie et environnement aquatique (GRIL), Montréal, Québec, Canada 3 Département des sciences biologiques, Université du Québec à Montréal, Québec, Canada. 4 Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, Québec, Canada 5 Département de géomatique appliquée, Université de Sherbrooke, Sherbrooke, Québec, Canada Corresponding author: David Walsh, Department of Biology, Concordia University, 7141 Sherbrooke St. West Montreal, QC H4B 1R6 Canada 514-848-2424 ext 3477 [email protected] Running title: Sub-ice Verrucomicrobia genomes in Quebec lakes bioRxiv preprint doi: https://doi.org/10.1101/324970; this version posted May 17, 2018. 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 Summary 2 Northern lakes are ice-covered for a large part of the year, yet our understanding 3 of microbial diversity and activity during winter lags behind that of the ice-free period. In 4 this study, we investigated under-ice diversity and metabolism of Verrucomicrobia in 5 seasonally ice-covered lakes in temperate and boreal regions of Quebec, Canada using 6 16S rRNA sequencing, metagenomics and metatranscriptomics. -
Development of the Equine Hindgut Microbiome in Semi-Feral and Domestic Conventionally-Managed Foals Meredith K
Tavenner et al. Animal Microbiome (2020) 2:43 Animal Microbiome https://doi.org/10.1186/s42523-020-00060-6 RESEARCH ARTICLE Open Access Development of the equine hindgut microbiome in semi-feral and domestic conventionally-managed foals Meredith K. Tavenner1, Sue M. McDonnell2 and Amy S. Biddle1* Abstract Background: Early development of the gut microbiome is an essential part of neonate health in animals. It is unclear whether the acquisition of gut microbes is different between domesticated animals and their wild counterparts. In this study, fecal samples from ten domestic conventionally managed (DCM) Standardbred and ten semi-feral managed (SFM) Shetland-type pony foals and dams were compared using 16S rRNA sequencing to identify differences in the development of the foal hindgut microbiome related to time and management. Results: Gut microbiome diversity of dams was lower than foals overall and within groups, and foals from both groups at Week 1 had less diverse gut microbiomes than subsequent weeks. The core microbiomes of SFM dams and foals had more taxa overall, and greater numbers of taxa within species groups when compared to DCM dams and foals. The gut microbiomes of SFM foals demonstrated enhanced diversity of key groups: Verrucomicrobia (RFP12), Ruminococcaceae, Fusobacterium spp., and Bacteroides spp., based on age and management. Lactic acid bacteria Lactobacillus spp. and other Lactobacillaceae genera were enriched only in DCM foals, specifically during their second and third week of life. Predicted microbiome functions estimated computationally suggested that SFM foals had higher mean sequence counts for taxa contributing to the digestion of lipids, simple and complex carbohydrates, and protein. -
Diversity in the Extracellular Vesicle-Derived Microbiome of Tissues According to Tumor Progression in Pancreatic Cancer
cancers Article Diversity in the Extracellular Vesicle-Derived Microbiome of Tissues According to Tumor Progression in Pancreatic Cancer Jin-Yong Jeong 1, Tae-Bum Kim 2 , Jinju Kim 1, Hwi Wan Choi 1, Eo Jin Kim 1, Hyun Ju Yoo 1 , Song Lee 3, Hye Ryeong Jun 3, Wonbeak Yoo 4 , Seokho Kim 5, Song Cheol Kim 3,6,* and Eunsung Jun 1,3,* 1 Department of Convergence Medicine, Asan Institute for Life Sciences, University of Ulsan College of Medicine and Asan Medical Center, Seoul 05505, Korea; [email protected] (J.-Y.J.); [email protected] (J.K.); [email protected] (H.W.C.); [email protected] (E.J.K.); [email protected] (H.J.Y.) 2 Department of Allergy and Clinical Immunology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; [email protected] 3 Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; [email protected] (S.L.); [email protected] (H.R.J.) 4 Environmental Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; [email protected] 5 Department of Medicinal Biotechnology, College of Health Sciences, Dong-A University, Busan 49315, Korea; [email protected] 6 Biomedical Engineering Research Center, Asan Institute of Life Science, AMIST, Asan Medical Center, Seoul 05505, Korea * Correspondence: [email protected] (S.C.K.); [email protected] (E.J.); Tel.: +82-2-3010-3936 (S.C.K.); +82-2-3010-1696 (E.J.); Fax: +82-2-474-9027 (S.C.K.); +82-2-474-9027 (E.J.) Received: 13 July 2020; Accepted: 17 August 2020; Published: 19 August 2020 Abstract: This study was conducted to identify the composition and diversity of the microbiome in tissues of pancreatic cancer and to determine its role. -
Card Uses a Minor Groove Wedge Mechanism to Stabilize the RNA
1 CarD uses a minor groove wedge mechanism to stabilize the RNA 2 polymerase open promoter complex 3 4 Brian Bae1, James Chen1, Elizabeth Davis1, Katherine Leon1, Seth A. Darst1,*, 5 Elizabeth A. Campbell1,* 6 7 1The Rockefeller University, Laboratory for Molecular Biophysics, 1230 York Avenue, New York, 8 NY 10065, USA. 9 10 *Correspondence to: E-mail: [email protected], [email protected] 11 12 Present Address: Elizabeth Davis, The University of Minnesota School of Medicine, 13 420 Delaware St. SE, Minneapolis, MN 55455, USA; Katherine Leon, Department of 14 Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, GCIS 15 W219 Chicago, IL 60637, USA. 16 17 2 18 Abstract A key point to regulate gene expression is at transcription initiation, and 19 activators play a major role. CarD, an essential activator in Mycobacterium tuberculosis, 20 is found in many bacteria, including Thermus species, but absent in Escherichia coli. To 21 delineate the molecular mechanism of CarD, we determined crystal structures of 22 Thermus transcription initiation complexes containing CarD. The structures show CarD 23 interacts with the unique DNA topology presented by the upstream double- 24 stranded/single-stranded DNA junction of the transcription bubble. We confirm that our 25 structures correspond to functional activation complexes, and extend our understanding 26 of the role of a conserved CarD Trp residue that serves as a minor groove wedge, 27 preventing collapse of the transcription bubble to stabilize the transcription initiation 28 complex. Unlike E. coli RNAP, many bacterial RNAPs form unstable promoter 29 complexes, explaining the need for CarD. -
Yu-Chen Ling and John W. Moreau
Microbial Distribution and Activity in a Coastal Acid Sulfate Soil System Introduction: Bioremediation in Yu-Chen Ling and John W. Moreau coastal acid sulfate soil systems Method A Coastal acid sulfate soil (CASS) systems were School of Earth Sciences, University of Melbourne, Melbourne, VIC 3010, Australia formed when people drained the coastal area Microbial distribution controlled by environmental parameters Microbial activity showed two patterns exposing the soil to the air. Drainage makes iron Microbial structures can be grouped into three zones based on the highest similarity between samples (Fig. 4). Abundant populations, such as Deltaproteobacteria, kept constant activity across tidal cycling, whereas rare sulfides oxidize and release acidity to the These three zones were consistent with their geological background (Fig. 5). Zone 1: Organic horizon, had the populations changed activity response to environmental variations. Activity = cDNA/DNA environment, low pH pore water further dissolved lowest pH value. Zone 2: surface tidal zone, was influenced the most by tidal activity. Zone 3: Sulfuric zone, Abundant populations: the heavy metals. The acidity and toxic metals then Method A Deltaproteobacteria Deltaproteobacteria this area got neutralized the most. contaminate coastal and nearby ecosystems and Method B 1.5 cause environmental problems, such as fish kills, 1.5 decreased rice yields, release of greenhouse gases, Chloroflexi and construction damage. In Australia, there is Gammaproteobacteria Gammaproteobacteria about a $10 billion “legacy” from acid sulfate soils, Chloroflexi even though Australia is only occupied by around 1.0 1.0 Cyanobacteria,@ Acidobacteria Acidobacteria Alphaproteobacteria 18% of the global acid sulfate soils. Chloroplast Zetaproteobacteria Rare populations: Alphaproteobacteria Method A log(RNA(%)+1) Zetaproteobacteria log(RNA(%)+1) Method C Method B 0.5 0.5 Cyanobacteria,@ Bacteroidetes Chloroplast Firmicutes Firmicutes Bacteroidetes Planctomycetes Planctomycetes Ac8nobacteria Fig. -
Analyse Bibliographique Sur Le Microbiote Intestinal Et Son Etude Dans Des Modeles Animaux De Maladies Metaboliques, En Particulier Chez Le Primate Non Humain These
VETAGRO SUP CAMPUS VETERINAIRE DE LYON Année 2019 - Thèse n°111 ANALYSE BIBLIOGRAPHIQUE SUR LE MICROBIOTE INTESTINAL ET SON ETUDE DANS DES MODELES ANIMAUX DE MALADIES METABOLIQUES, EN PARTICULIER CHEZ LE PRIMATE NON HUMAIN THESE Présentée à l’UNIVERSITE CLAUDE-BERNARD - LYON I (Médecine - Pharmacie) et soutenue publiquement le 6 décembre 2019 pour obtenir le grade de Docteur Vétérinaire par SCHUTZ Charlotte Née le 5 mars 1994 à Zürich (Suisse) VETAGRO SUP CAMPUS VETERINAIRE DE LYON Année 2019 - Thèse n°111 ANALYSE BIBLIOGRAPHIQUE SUR LE MICROBIOTE INTESTINAL ET SON ETUDE DANS DES MODELES ANIMAUX DE MALADIES METABOLIQUES, EN PARTICULIER CHEZ LE PRIMATE NON HUMAIN THESE Présentée à l’UNIVERSITE CLAUDE-BERNARD - LYON I (Médecine - Pharmacie) et soutenue publiquement le 6 décembre 2019 pour obtenir le grade de Docteur Vétérinaire par SCHUTZ Charlotte Née le 5 mars 1994 à Zürich (Suisse) Liste du corps enseignant Liste des Enseignants du Campus Vétérinaire de Lyon (01-09-2019) ABITBOL Marie DEPT-BASIC-SCIENCES Professeur ALVES-DE-OLIVEIRA Laurent DEPT-BASIC-SCIENCES Maître de conférences ARCANGIOLI Marie-Anne DEPT-ELEVAGE-SPV Professeur AYRAL Florence DEPT-ELEVAGE-SPV Maître de conférences BECKER Claire DEPT-ELEVAGE-SPV Maître de conférences BELLUCO Sara DEPT-AC-LOISIR-SPORT Maître de conférences BENAMOU-SMITH Agnès DEPT-AC-LOISIR-SPORT Maître de conférences BENOIT Etienne DEPT-BASIC-SCIENCES Professeur BERNY Philippe DEPT-BASIC-SCIENCES Professeur BONNET-GARIN Jeanne-Marie DEPT-BASIC-SCIENCES Professeur BOULOCHER Caroline DEPT-BASIC-SCIENCES -
Complete Genome Sequence of Akkermansia Glycaniphila Strain Pytt, a Mucin-Degrading Specialist of the Reticulated Python Gut
PROKARYOTES crossm Complete Genome Sequence of Akkermansia glycaniphila Strain PytT,a Mucin-Degrading Specialist of the Reticulated Python Gut Downloaded from Janneke P. Ouwerkerk,a Jasper J. Koehorst,b Peter J. Schaap,b Jarmo Ritari,d Lars Paulin,c Clara Belzer,a Willem M. de Vosa,d,e Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlandsa; Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlandsb; Institute of Biotechnology, University of Helsinki, Helsinki, Finlandc; Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finlandd; RPU Immunobiology, Department of Bacteriology & Immunology, University of Helsinki, Helsinki, Finlande ABSTRACT Akkermansia glycaniphila is a novel Akkermansia species that was iso- http://mra.asm.org/ lated from the intestine of the reticulated python and shares the capacity to de- Received 16 August 2016 Accepted 1 grade mucin with the human strain Akkermansia muciniphila MucT. Here, we report November 2016 Published 5 January 2017 Citation Ouwerkerk JP, Koehorst JJ, Schaap PJ, T the complete genome sequence of strain Pyt of 3,074,121 bp. The genomic analysis Ritari J, Paulin L, Belzer C, de Vos WM. 2017. reveals genes for mucin degradation and aerobic respiration. Complete genome sequence of Akkermansia glycaniphila strain PytT, a mucin-degrading specialist of the reticulated python gut. he ability to grow on mucin as a sole carbon and nitrogen source is a distinctive Genome Announc 5:e01098-16. https:// doi.org/10.1128/genomeA.01098-16. Tfeature of the human isolate Akkermansia muciniphila MucT (1). A. glycaniphila strain Copyright © 2017 Ouwerkerk et al. This is an T on February 21, 2019 by guest Pyt is the second Akkermansia species described to be mucolytic in pure culture (2).