Codium Fragile Ameliorates High-Fat Diet-Induced Metabolism by Modulating the Gut Microbiota in Mice
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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. -
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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. -
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. -
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. -
Modulation of the Gut Microbiota Alters the Tumour-Suppressive Efficacy of Tim-3 Pathway Blockade in a Bacterial Species- and Host Factor-Dependent Manner
microorganisms Article Modulation of the Gut Microbiota Alters the Tumour-Suppressive Efficacy of Tim-3 Pathway Blockade in a Bacterial Species- and Host Factor-Dependent Manner Bokyoung Lee 1,2, Jieun Lee 1,2, Min-Yeong Woo 1,2, Mi Jin Lee 1, Ho-Joon Shin 1,2, Kyongmin Kim 1,2 and Sun Park 1,2,* 1 Department of Microbiology, Ajou University School of Medicine, Youngtongku Wonchondong San 5, Suwon 442-749, Korea; [email protected] (B.L.); [email protected] (J.L.); [email protected] (M.-Y.W.); [email protected] (M.J.L.); [email protected] (H.-J.S.); [email protected] (K.K.) 2 Department of Biomedical Sciences, The Graduate School, Ajou University, Youngtongku Wonchondong San 5, Suwon 442-749, Korea * Correspondence: [email protected]; Tel.: +82-31-219-5070 Received: 22 August 2020; Accepted: 9 September 2020; Published: 11 September 2020 Abstract: T cell immunoglobulin and mucin domain-containing protein-3 (Tim-3) is an immune checkpoint molecule and a target for anti-cancer therapy. In this study, we examined whether gut microbiota manipulation altered the anti-tumour efficacy of Tim-3 blockade. The gut microbiota of mice was manipulated through the administration of antibiotics and oral gavage of bacteria. Alterations in the gut microbiome were analysed by 16S rRNA gene sequencing. Gut dysbiosis triggered by antibiotics attenuated the anti-tumour efficacy of Tim-3 blockade in both C57BL/6 and BALB/c mice. Anti-tumour efficacy was restored following oral gavage of faecal bacteria even as antibiotic administration continued. In the case of oral gavage of Enterococcus hirae or Lactobacillus johnsonii, transferred bacterial species and host mouse strain were critical determinants of the anti-tumour efficacy of Tim-3 blockade. -
Characterization of the First Cultured Representative of Verrucomicrobia Subdivision 5 Indicates the Proposal of a Novel Phylum
The ISME Journal (2016) 10, 2801–2816 OPEN © 2016 International Society for Microbial Ecology All rights reserved 1751-7362/16 www.nature.com/ismej ORIGINAL ARTICLE Characterization of the first cultured representative of Verrucomicrobia subdivision 5 indicates the proposal of a novel phylum Stefan Spring1, Boyke Bunk2, Cathrin Spröer3, Peter Schumann3, Manfred Rohde4, Brian J Tindall1 and Hans-Peter Klenk1,5 1Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; 2Department Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; 3Department Central Services, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany and 4Central Facility for Microscopy, Helmholtz-Centre of Infection Research, Braunschweig, Germany The recently isolated strain L21-Fru-ABT represents moderately halophilic, obligately anaerobic and saccharolytic bacteria that thrive in the suboxic transition zones of hypersaline microbial mats. Phylogenetic analyses based on 16S rRNA genes, RpoB proteins and gene content indicated that strain L21-Fru-ABT represents a novel species and genus affiliated with a distinct phylum-level lineage originally designated Verrucomicrobia subdivision 5. A survey of environmental 16S rRNA gene sequences revealed that members of this newly recognized phylum are wide-spread and ecologically important in various anoxic environments ranging from hypersaline sediments to wastewater and the intestine of animals. Characteristic phenotypic traits of the novel strain included the formation of extracellular polymeric substances, a Gram-negative cell wall containing peptidoglycan and the absence of odd-numbered cellular fatty acids. Unusual metabolic features deduced from analysis of the genome sequence were the production of sucrose as osmoprotectant, an atypical glycolytic pathway lacking pyruvate kinase and the synthesis of isoprenoids via mevalonate. -
Microbial Community Structure in Rice, Crops, and Pastures Rotation Systems with Different Intensification Levels in the Temperate Region of Uruguay
Supplementary Material Microbial community structure in rice, crops, and pastures rotation systems with different intensification levels in the temperate region of Uruguay Sebastián Martínez Table S1. Relative abundance of the 20 most abundant bacterial taxa of classified sequences. Relative Taxa Phylum abundance 4,90 _Bacillus Firmicutes 3,21 _Bacillus aryabhattai Firmicutes 2,76 _uncultured Prosthecobacter sp. Verrucomicrobia 2,75 _uncultured Conexibacteraceae bacterium Actinobacteria 2,64 _uncultured Conexibacter sp. Actinobacteria 2,14 _Nocardioides sp. Actinobacteria 2,13 _Acidothermus Actinobacteria 1,50 _Bradyrhizobium Proteobacteria 1,23 _Bacillus Firmicutes 1,10 _Pseudolabrys_uncultured bacterium Proteobacteria 1,03 _Bacillus Firmicutes 1,02 _Nocardioidaceae Actinobacteria 0,99 _Candidatus Solibacter Acidobacteria 0,97 _uncultured Sphingomonadaceae bacterium Proteobacteria 0,94 _Streptomyces Actinobacteria 0,91 _Terrabacter_uncultured bacterium Actinobacteria 0,81 _Mycobacterium Actinobacteria 0,81 _uncultured Rubrobacteria Actinobacteria 0,77 _Xanthobacteraceae_uncultured forest soil bacterium Proteobacteria 0,76 _Streptomyces Actinobacteria Table S2. Relative abundance of the 20 most abundant fungal taxa of classified sequences. Relative Taxa Orden abundance. 20,99 _Fusarium oxysporum Ascomycota 11,97 _Aspergillaceae Ascomycota 11,14 _Chaetomium globosum Ascomycota 10,03 _Fungi 5,40 _Cucurbitariaceae; uncultured fungus Ascomycota 5,29 _Talaromyces purpureogenus Ascomycota 3,87 _Neophaeosphaeria; uncultured fungus Ascomycota -
Microbial Life Under Ice: Metagenome Diversity and in Situ Activity of Verrucomicrobia in Seasonally Ice-Covered Lakes Patricia
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. -
Long-Term Blackcurrant Supplementation Modified Gut
nutrients Article Long-Term Blackcurrant Supplementation Modified Gut Microbiome Profiles in Mice in an Age-Dependent Manner: An Exploratory Study 1, 2, 3 3 4 Lei Cao y, Sang Gil Lee y, Melissa M. Melough , Junichi R. Sakaki , Kendra R. Maas , Sung I. Koo 3 and Ock K. Chun 3,* 1 Institute of Marine Life Sciences, Pukyong National University, Busan 48513, Korea; [email protected] 2 Department of Food Science and Nutrition, Pukyong National University, Busan 48513, Korea; [email protected] 3 Department of Nutritional Sciences, University of Connecticut, Storrs, CT 06269, USA; [email protected] (M.M.M.); [email protected] (J.R.S.); [email protected] (S.I.K.) 4 Microbial Analysis, Resources and Services (MARS), University of Connecticut, Storrs, CT 06269, USA; [email protected] * Correspondence: [email protected] These authors contributed equally to this work. y Received: 12 December 2019; Accepted: 20 January 2020; Published: 21 January 2020 Abstract: Recent studies have suggested that blackcurrant (BC) anthocyanins have promising health benefits, possibly through regulating gut microbiome. Three- and eighteen-month old female mice were fed standard mouse diets for 4 months, each with or without BC (1% w/w) supplementation (n = 3 in each treatment group, 12 in total). We then assessed gut microbiome profiles using 16S sequencing of their feces. Old mice had a less diverse microbiome community compared to young mice and there was a remarkable age-related difference in microbiome composition in the beta diversity analysis. BC supplementation did not significantly affect alpha or beta diversity. The relative abundance of several phyla, including Firmicutes, Bacteroidetes, Proteobacteria and Tenericutes, was lower in old mice. -
First Insights Into the Fecal Bacterial Microbiota of the Black–Tailed Prairie Dog (Cynomys Ludovicianus) in Janos, Mexico I
Animal Biodiversity and Conservation 42.1 (2019) 127 First insights into the fecal bacterial microbiota of the black–tailed prairie dog (Cynomys ludovicianus) in Janos, Mexico I. Pacheco–Torres, C. García–De la Peña, D. R. Aguillón–Gutiérrez, C. A. Meza–Herrera, F. Vaca–Paniagua, C. E. Díaz–Velásquez, L. M. Valenzuela–Núñez, V. Ávila–Rodríguez Pacheco–Torres, I., García–De la Peña, C., Aguillón–Gutiérrez, D. R., Meza–Herrera, C. A., Vaca–Paniagua, F., Díaz–Velásquez, C. E., Valenzuela–Núñez, L. M., Ávila–Rodríguez, V., 2019. First insights into the fecal bacte- rial microbiota of the black–tailed prairie dog (Cynomys ludovicianus) in Janos, Mexico. Animal Biodiversity and Conservation, 42.1: 127–134, Doi: https://doi.org/10.32800/abc.2019.42.0127 Abstract First insights into the fecal bacterial microbiota of the black–tailed prairie dog (Cynomys ludovicianus) in Janos, Mexico. Intestinal bacteria are an important indicator of the health of their host. Incorporating periodic assess- ment of the taxonomic composition of these microorganisms into management and conservation plans can be a valuable tool to detect changes that may jeopardize the survival of threatened populations. Here we describe the diversity and abundance of fecal bacteria for the black–tailed prairie dog (Cynomys ludovicianus), a threat- ened species, in the Janos Biosphere Reserve, Chihuahua, Mexico. We analyzed fecal samples through next generation massive sequencing and amplified the V3–V4 region of the 16S rRNA gene using Illumina technology. The results were analyzed with QIIME based on the EzBioCloud reference. We identified 12 phyla, 22 classes, 33 orders, 54 families and 263 genera. -
Interactions Between Host Genetics and Gut Microbiota Determine Susceptibility to CNS Autoimmunity
Interactions between host genetics and gut microbiota determine susceptibility to CNS autoimmunity Theresa L. Montgomerya,1, Axel Künstnerb,c,1, Josephine J. Kennedya, Qian Fangd, Lori Asariand, Rachel Culp-Hille, Angelo D’Alessandroe, Cory Teuscherd, Hauke Buschb,c, and Dimitry N. Krementsova,2 aDepartment of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05401; bMedical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, 23562 Lübeck, Germany; cInstitute for Cardiogenetics, University of Lübeck, 23562 Lübeck, Germany; dDepartment of Medicine, Immunobiology Division, University of Vermont, Burlington, VT 05401; and eDepartment of Biochemistry and Molecular Genetics, University of Colorado, Aurora, CO 80045 Edited by Dennis L. Kasper, Harvard Medical School, Boston, MA, and approved August 26, 2020 (received for review February 23, 2020) Multiple sclerosis (MS) is an autoimmune disease of the central circulation to directly impact distal sites, including the brain (11, nervous system. The etiology of MS is multifactorial, with disease 12). With regard to MS, a number of recent case-control studies risk determined by genetics and environmental factors. An emerg- have demonstrated that the gut microbiome of MS patients differs ing risk factor for immune-mediated diseases is an imbalance from that of their healthy control counterparts. Some broad fea- in the gut microbiome. However, the identity of gut microbes as- tures, such as decreased abundance of putative short-chain fatty sociated with disease risk, their mechanisms of action, and the acid (SCFA)-producing bacteria and expansion of Akkermansia, interactions with host genetics remain obscure. To address these have been observed consistently across several studies (13–19). -
Genomic Characterization of the Uncultured Bacteroidales Family S24-7 Inhabiting the Guts of Homeothermic Animals Kate L
Ormerod et al. Microbiome (2016) 4:36 DOI 10.1186/s40168-016-0181-2 RESEARCH Open Access Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals Kate L. Ormerod1, David L. A. Wood1, Nancy Lachner1, Shaan L. Gellatly2, Joshua N. Daly1, Jeremy D. Parsons3, Cristiana G. O. Dal’Molin4, Robin W. Palfreyman4, Lars K. Nielsen4, Matthew A. Cooper5, Mark Morrison6, Philip M. Hansbro2 and Philip Hugenholtz1* Abstract Background: Our view of host-associated microbiota remains incomplete due to the presence of as yet uncultured constituents. The Bacteroidales family S24-7 is a prominent example of one of these groups. Marker gene surveys indicate that members of this family are highly localized to the gastrointestinal tracts of homeothermic animals and are increasingly being recognized as a numerically predominant member of the gut microbiota; however, little is known about the nature of their interactions with the host. Results: Here, we provide the first whole genome exploration of this family, for which we propose the name “Candidatus Homeothermaceae,” using 30 population genomes extracted from fecal samples of four different animal hosts: human, mouse, koala, and guinea pig. We infer the core metabolism of “Ca. Homeothermaceae” to be that of fermentative or nanaerobic bacteria, resembling that of related Bacteroidales families. In addition, we describe three trophic guilds within the family, plant glycan (hemicellulose and pectin), host glycan, and α-glucan, each broadly defined by increased abundance of enzymes involved in the degradation of particular carbohydrates. Conclusions: “Ca. Homeothermaceae” representatives constitute a substantial component of the murine gut microbiota, as well as being present within the human gut, and this study provides important first insights into the nature of their residency.