Title Isolation and Identification Methods for Solobacterium Moorei
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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). -
Oral Microbiome Composition Reflects Prospective Risk for Esophageal Cancers
Cancer Prevention and Epidemiology Research Oral Microbiome Composition Reflects Prospective Risk for Esophageal Cancers Brandilyn A. Peters1, Jing Wu1,2, Zhiheng Pei2,3,4, Liying Yang5, Mark P. Purdue6, Neal D. Freedman6, Eric J. Jacobs7, Susan M. Gapstur7, Richard B. Hayes1,2, and Jiyoung Ahn1,2 Abstract Bacteria may play a role in esophageal adenocarcinoma (EAC) conditional logistic regression adjusting for BMI, smoking, and and esophageal squamous cell carcinoma (ESCC), although alcohol. We found the periodontal pathogen Tannerella forsythia evidence is limited to cross-sectional studies. In this study, we to be associated with higher risk of EAC. Furthermore, we found examined the relationship of oral microbiota with EAC and ESCC that depletion of the commensal genus Neisseria and the species risk in a prospective study nested in two cohorts. Oral bacteria Streptococcus pneumoniae was associated with lower EAC risk. were assessed using 16S rRNA gene sequencing in prediagnostic Bacterial biosynthesis of carotenoids was also associated with mouthwash samples from n ¼ 81/160 EAC and n ¼ 25/50 ESCC protection against EAC. Finally, the abundance of the periodontal cases/matched controls. Findings were largely consistent across pathogen Porphyromonas gingivalis trended with higher risk of ESCC. both cohorts. Metagenome content was predicted using PiCRUST. Overall, our findings have potential implications for the early We examined associations between centered log-ratio trans- detection and prevention of EAC and ESCC. Cancer Res; 77(23); formed taxon or functional pathway abundances and risk using 6777–87. Ó2017 AACR. Introduction intake, and smoking for EAC, and alcohol drinking, low fruit/ vegetable intake, and smoking for ESCC (4), but the etiology Esophageal cancer is the eighth most common cancer and sixth of these diseases cannot be fully explained by these factors. -
The Gut Microbiome in Atherosclerotic Cardiovascular Disease Yangqing Peng Et Al
Washington University School of Medicine Digital Commons@Becker Open Access Publications 2017 The gut microbiome in atherosclerotic cardiovascular disease Yangqing Peng et al Follow this and additional works at: https://digitalcommons.wustl.edu/open_access_pubs Recommended Citation Peng, Yangqing and et al, ,"The gut microbiome in atherosclerotic cardiovascular disease." Nature Communications.8,. (2017). https://digitalcommons.wustl.edu/open_access_pubs/6294 This Open Access Publication is brought to you for free and open access by Digital Commons@Becker. It has been accepted for inclusion in Open Access Publications by an authorized administrator of Digital Commons@Becker. For more information, please contact [email protected]. ARTICLE DOI: 10.1038/s41467-017-00900-1 OPEN The gut microbiome in atherosclerotic cardiovascular disease Zhuye Jie1,2,3, Huihua Xia1,2, Shi-Long Zhong4,5, Qiang Feng1,2,6,7,17, Shenghui Li1, Suisha Liang1,2, Huanzi Zhong 1,2,3,7, Zhipeng Liu1,8, Yuan Gao1,2, Hui Zhao1, Dongya Zhang1, Zheng Su1, Zhiwei Fang1, Zhou Lan1, Junhua Li 1,2,3,9, Liang Xiao1,2,6, Jun Li1, Ruijun Li10, Xiaoping Li1,2, Fei Li1,2,8, Huahui Ren1, Yan Huang1, Yangqing Peng1,18, Guanglei Li1, Bo Wen 1,2, Bo Dong1, Ji-Yan Chen4, Qing-Shan Geng4, Zhi-Wei Zhang4, Huanming Yang1,2,11, Jian Wang1,2,11, Jun Wang1,12,19, Xuan Zhang 13, Lise Madsen 1,2,7,14, Susanne Brix 15, Guang Ning16, Xun Xu1,2, Xin Liu 1,2, Yong Hou 1,2, Huijue Jia 1,2,3,12, Kunlun He10 & Karsten Kristiansen1,2,7 The gut microbiota has been linked to cardiovascular diseases. -
Antimicrobial Activity of Streptococcus Salivarius K12 on Bacteria Involved
a r c h i v e s o f o r a l b i o l o g y 5 7 ( 2 0 1 2 ) 1 0 4 1 – 1 0 4 7 Available online at www.sciencedirect.com journal homepage: http://www.elsevier.com/locate/aob Antimicrobial activity of Streptococcus salivarius K12 on bacteria involved in oral malodour a a a, a b a L. Masdea , E.M. Kulik , I. Hauser-Gerspach *, A.M. Ramseier , A. Filippi , T. Waltimo a Institute of Preventive Dentistry and Oral Microbiology, School of Dental Medicine, University of Basel, Switzerland b Department of Oral Surgery, Oral Radiology and Oral Medicine and the Centre of Dental Traumatology, School of Dental Medicine, University of Basel, Switzerland a r t i c l e i n f o a b s t r a c t Article history: Objective: To investigate the antimicrobial activity of the bacteriocin-producing strain Accepted 11 February 2012 Streptococcus salivarius K12 against several bacteria involved in halitosis. Design: The inhibitory activity of S. salivarius K12 against Solobacterium moorei CCUG39336, Keywords: four clinical S. moorei isolates, Atopobium parvulum ATCC33793 and Eubacterium sulci ATCC35585 was examined by a deferred antagonism test. Eubacterium saburreum ATCC33271 Streptococcus salivarius K12 Halitosis and Parvimonas micra ATCC33270, which have been tested in previous studies, served as positive controls, and the Gram-negative strain Bacteroides fragilis ZIB2800 served as a Solobacterium moorei negative control. Additionally, the occurrence of resistance in S. moorei CCUG39336 to S. Deferred antagonism test Bacteriocin salivarius K12 was analysed by either direct plating or by passage of S. -
Investigation and Subsequent Manipulation of The
Investigation and subsequent manipulation of the intestinal microbiota of pigs, with a view to optimising feed efficiency By Ursula Mary McCormack (B.Ag.Sc) A thesis submitted for the degree of Doctor of Philosophy Waterford Institute of Technology Research Supervisors Dr. Gillian E. Gardiner Dr. Peadar G. Lawlor Submitted to Waterford Institute of Technology September 2017 Declaration No element of the work described in this thesis has been previously submitted for a degree at this or any other institution. The work in this thesis has been performed entirely by the author. Signature: ____________________________ Date: ___________________________ i Table of Contents Declaration ..................................................................................................................... i Table of Tables ............................................................................................................. xi Table of Figures .......................................................................................................... xiii List of abbreviations ................................................................................................... xvi Abstract ............................................................................................................................. 1 1. Literature Review .......................................................................................................... 2 1.1 Introduction ............................................................................................................ -
Uncovering Complex Microbiome Activities Via Metatranscriptomics
Edlund et al. Microbiome (2018) 6:217 https://doi.org/10.1186/s40168-018-0591-4 RESEARCH Open Access Uncovering complex microbiome activities via metatranscriptomics during 24 hours of oral biofilm assembly and maturation Anna Edlund1* , Youngik Yang2, Shibu Yooseph3, Xuesong He4, Wenyuan Shi4 and Jeffrey S. McLean5* Abstract Background: Dental plaque is composed of hundreds of bacterial taxonomic units and represents one of the most diverse and stable microbial ecosystems associated with the human body. Taxonomic composition and functional capacity of mature plaque is gradually shaped during several stages of community assembly via processes such as co-aggregation, competition for space and resources, and by bacterially produced reactive agents. Knowledge on the dynamics of assembly within complex communities is very limited and derives mainly from studies composed of a limited number of bacterial species. To fill current knowledge gaps, we applied parallel metagenomic and metatranscriptomic analyses during assembly and maturation of an in vitro oral biofilm. This model system has previously demonstrated remarkable reproducibility in taxonomic composition across replicate samples during maturation. Results: Time course analysis of the biofilm maturation was performed by parallel sampling every 2–3 h for 24 h for both DNA and RNA. Metagenomic analyses revealed that community taxonomy changed most dramatically between three and six hours of growth when pH dropped from 6.5 to 5.5. By applying comparative metatranscriptome analysis we could identify major shifts in overall community activities between six and nine hours of growth when pH dropped below 5.5, as 29,015 genes were significantly up- or down- expressed. -
Gut Microbiome Profiles and Associated Metabolic Pathways in HIV-Infected Treatment-Naïve Patients
cells Article Gut Microbiome Profiles and Associated Metabolic Pathways in HIV-Infected Treatment-Naïve Patients Wellinton M. do Nascimento 1,2, Aline Machiavelli 1,2 , Luiz G. E. Ferreira 3, Luisa Cruz Silveira 1 , Suwellen S. D. de Azevedo 4 , Gonzalo Bello 4, Daniel P. Smith 5 , Melissa P. Mezzari 5 , Joseph F. Petrosino 5, Rubens Tadeu Delgado Duarte 6, Carlos R. Zárate-Bladés 2,*,†, and Aguinaldo R. Pinto 1,† 1 Laboratório de Imunologia Aplicada, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Campus Universitário da Trindade, Florianópolis, SC 88034-040, Brazil; [email protected] (W.M.d.N.); [email protected] (A.M.); [email protected] (L.C.S.); [email protected] (A.R.P.) 2 Laboratório de Imunorregulação, 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; [email protected] 4 Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Av. Brasil, 4365, Rio de Janeiro, RJ 21045-900, Brazil; [email protected] (S.S.D.d.A.); gbello@ioc.fiocruz.br (G.B.) 5 Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; [email protected] (D.P.S.); [email protected] (M.P.M.); [email protected] (J.F.P.) 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; [email protected] Citation: do Nascimento, W.M.; * Correspondence: [email protected]; Tel.: +55-48-37215210 Machiavelli, A.; Ferreira, L.G.E.; Cruz † These authors contributed equally to this work. -
Dakotella Fusiforme Gen. Nov., Sp. Nov., Isolated from Healthy Human Feces
Description of a new member of the family Erysipelotrichaceae: Dakotella fusiforme gen. nov., sp. nov., isolated from healthy human feces Sudeep Ghimire, Supapit Wongkuna and Joy Scaria Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, United States of America ABSTRACT A Gram-positive, non-motile, rod-shaped facultative anaerobic bacterial strain SG502T was isolated from healthy human fecal samples in Brookings, SD, USA. The comparison of the 16S rRNA gene placed the strain within the family Erysipelotrichaceae. Within this family, Clostridium innocuum ATCC 14501T, Longicatena caecimuris strain PG- 426-CC-2, Eubacterium dolichum DSM 3991T and E. tortuosum DSM 3987T (=ATCC 25548T) were its closest taxa with 95.28%, 94.17%, 93.25%, and 92.75% 16S rRNA sequence identities respectively. The strain SG502T placed itself close to C. innocuum in the 16S rRNA phylogeny. The members of genus Clostridium within family Erysipelotrichaceae was proposed to be reassigned to genus Erysipelatoclostridium to resolve the misclassification of genus Clostridium. Therefore, C. innocuum was also classified into this genus temporarily with the need to reclassify it in the future because of its difference in genomic properties. Similarly, genome sequencing of the strain and comparison with its 16S phylogenetic members and proposed members of the genus Erysipelatoclostridium, SG502T warranted a separate genus even though its 16S rRNA similarity was >95% when comapred to C. innocuum. The strain was 71.8% similar at ANI, 19.8% [17.4–22.2%] at dDDH and 69.65% similar at AAI to its closest neighbor C. innocuum. The genome size was nearly 2,683,792 bp with 32.88 mol% G+C content, Submitted 19 November 2019 which is about half the size of C. -
Gut Microbiome-Related Effects of Berberine and Probiotics on Type 2 Diabetes (The PREMOTE Study)
ARTICLE https://doi.org/10.1038/s41467-020-18414-8 OPEN Gut microbiome-related effects of berberine and probiotics on type 2 diabetes (the PREMOTE study) Yifei Zhang 1,19, Yanyun Gu1,19, Huahui Ren2,19, Shujie Wang 1,19, Huanzi Zhong 2,19, Xinjie Zhao3, Jing Ma4, Xuejiang Gu5, Yaoming Xue6, Shan Huang7, Jialin Yang8, Li Chen9, Gang Chen10, Shen Qu11, Jun Liang12, Li Qin13, Qin Huang14, Yongde Peng15,QiLi3, Xiaolin Wang3, Ping Kong2, Guixue Hou 2, Mengyu Gao2, Zhun Shi2, Xuelin Li1, Yixuan Qiu1, Yuanqiang Zou2, Huanming Yang2,16, Jian Wang2,16, ✉ ✉ Guowang Xu3, Shenghan Lai17, Junhua Li 2,18 , Guang Ning1 & Weiqing Wang1 1234567890():,; Human gut microbiome is a promising target for managing type 2 diabetes (T2D). Measures altering gut microbiota like oral intake of probiotics or berberine (BBR), a bacteriostatic agent, merit metabolic homoeostasis. We hence conducted a randomized, double-blind, placebo- controlled trial with newly diagnosed T2D patients from 20 centres in China. Four-hundred- nine eligible participants were enroled, randomly assigned (1:1:1:1) and completed a 12-week treatment of either BBR-alone, probiotics+BBR, probiotics-alone, or placebo, after a one-week run-in of gentamycin pretreatment. The changes in glycated haemoglobin, as the primary outcome, in the probiotics+BBR (least-squares mean [95% CI], −1.04[−1.19, −0.89]%) and BBR-alone group (−0.99[−1.16, −0.83]%) were significantly greater than that in the placebo and probiotics-alone groups (−0.59[−0.75, −0.44]%, −0.53[−0.68, −0.37]%, P < 0.001). BBR treatment induced more gastrointestinal side effects. -
Phylogenic and Phenotypic Characterization of Some Eubacterium-Like Isolates from Human Feces: Description of Solobacterium Moorei Gen
Microbiol. Immunol., 44(4), 223-227, 2000 Phylogenic and Phenotypic Characterization of Some Eubacterium-Like Isolates from Human Feces: Description of Solobacterium moorei Gen. Nov., Sp. Nov. Akiko Kageyama*, and Yoshimi Benno Japan Collection of Microorganisms, The Institute of Physical and Chemical Research (RIKEN), Wako, Saitama 351-0198, Japan Received October 13, 1999; in revised form, December 9, 1999. Accepted January 10, 2000 Abstract: Three isolated strains from human feces were characterized by biochemical tests and 16S rDNA analysis. Phylogenetic analysis revealed that these isolated strains were members of the Clostridium sub- phylum of Gram-positive bacteria. The phenotypic characters resembled those of the genus Eubacterium, but these strains were shown to be phylogenetically distant from the type species of the genus, Eubacteri- um limosum. The strains showed a specific phylogenetic association with Holdemania filiformis and Erysipelothrix rhusiopathiae. Based on a 16S rDNA sequence divergence of greater than 12% with H. fili- formis and E. rhusiopathiae, a new genus, Solobacterium, is proposed for three strains, with one species, Solobacterium moorei. The type strain of Solobacterium moorei is JCM 106451. Key words: Solobacterium moorei gen. nov., sp. nov., 16S rDNA The genus Eubacterium contains all Gram-positive, On the basis of the results presented, we propose that anaerobic, non-spore-forming, rod-shaped bacteria which these strains be classified as Solobacterium moorei gen. do not belong to the genera Propionibacterium, Lacto- nov., sp. nov. bacillus, or Bifzdobacterium. Differentiation among these genera is based on fermentation products from glucose: Materials and Methods propionic acid as a major end product for Propionibac- terium, lactic acid as a major product for Lactobacillus, Bacterial strains studied and cultivation. -
A New Look at the Genus Solobacterium: a Retrospective Analysis of Twenty-Seven Cases of Infection Involving S
microorganisms Article A New Look at the Genus Solobacterium: A Retrospective Analysis of Twenty-Seven Cases of Infection Involving S. moorei and a Review of Sequence Databases and the Literature Corentine Alauzet 1 , Fabien Aujoulat 2, Alain Lozniewski 1, Safa Ben Brahim 3, Chloé Domenjod 4, Cécilia Enault 4 , Jean-Philippe Lavigne 5 and Hélène Marchandin 6,* 1 Laboratoire SIMPA Stress Immunité Pathogènes EA 7300, Université de Lorraine, & Service de Microbiologie, CHRU de Nancy, 54500 Vandœuvre-lès-Nancy, France; [email protected] (C.A.); [email protected] (A.L.) 2 HydroSciences Montpellier, CNRS, IRD, Université de Montpellier, 34093 Montpellier, France; [email protected] 3 Service de Microbiologie, CHRU de Nancy, 54500 Vandœuvre-lès-Nancy, France; [email protected] 4 Service de Microbiologie et Hygiène Hospitalière, CHU de Nîmes, 30029 Nîmes, France; [email protected] (C.D.); [email protected] (C.E.) 5 VBIC, INSERM U1047, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 30029 Nîmes, France; [email protected] 6 HydroSciences Montpellier, CNRS, IRD, Université de Montpellier, Service de Microbiologie et Hygiène Citation: Alauzet, C.; Aujoulat, F.; Hospitalière, CHU de Nîmes, 30029 Nîmes, France Lozniewski, A.; Ben Brahim, S.; * Correspondence: [email protected] Domenjod, C.; Enault, C.; Lavigne, J.-P.; Marchandin, H. A New Abstract: Solobacterium moorei is an anaerobic Gram-positive bacillus present within the oral and Look at the Genus Solobacterium: the intestinal microbiota that has rarely been described in human infections. Besides its role in A Retrospective Analysis of halitosis and oral infections, S. -
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Published OnlineFirst October 29, 2018; DOI: 10.1158/1055-9965.EPI-18-0542 Research Article Cancer Epidemiology, Biomarkers The Microbiomes of Pancreatic and Duodenum & Prevention Tissue Overlap and Are Highly Subject Specific but Differ between Pancreatic Cancer and Noncancer Subjects Erika del Castillo1,4, Richard Meier2, Mei Chung1, Devin C. Koestler2,3, Tsute Chen4, Bruce J. Paster4,5, Kevin P. Charpentier6, Karl T. Kelsey7, Jacques Izard8,9, and Dominique S. Michaud1 Abstract Background: In mice, bacteria from the mouth can trans- cavity. Bacterial DNA across different sites in the pancreas and locate to the pancreas and impact pancreatic cancer progres- duodenum were highly subject specific in both cancer and sion. In humans, oral bacteria associated with periodontal noncancer subjects. Presence of genus Lactobacillus was signif- disease have been linked to pancreatic cancer risk. It is not icantly higher in noncancer subjects compared with cancer known if DNA bacterial profiles in the pancreas and duode- subjects and the relative abundance of Fusobacterium spp., num are similar within individuals. previously associated with colorectal cancer, was higher in Methods: Tissue samples were obtained from 50 subjects cancer subjects compared with noncancer subjects. with pancreatic cancer or other conditions requiring foregut Conclusions: Bacterial DNA profiles in the pancreas were surgery at the Rhode Island Hospital (RIH), and from 34 similar to those in the duodenum tissue of the same subjects, organs obtained from the National Disease Research Inter- regardless of disease state, suggesting that bacteria may be change. 16S rRNA gene sequencing was performed on 189 migrating from the gut into the pancreas. Whether bacteria tissue samples (pancreatic duct, duodenum, pancreas), 57 play a causal role in human pancreatic cancer needs to be swabs (bile duct, jejunum, stomach), and 12 stool samples.