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Li et al. Microbiome (2021) 9:47 https://doi.org/10.1186/s40168-020-00995-7 RESEARCH Open Access Characterization of the human skin resistome and identification of two microbiota cutotypes Zhiming Li1,2†, Jingjing Xia3,4,5†, Liuyiqi Jiang3†, Yimei Tan4,6†, Yitai An1,2, Xingyu Zhu4,7, Jie Ruan1,2, Zhihua Chen1,2, Hefu Zhen1,2, Yanyun Ma4,7, Zhuye Jie1,2, Liang Xiao1,2, Huanming Yang1,2, Jian Wang1,2, Karsten Kristiansen1,2,8, Xun Xu1,2,9, Li Jin4,10, Chao Nie1,2*, Jean Krutmann4,5,11*, Xiao Liu1,12,13* and Jiucun Wang3,4,10,14* Abstract Background: The human skin microbiota is considered to be essential for skin homeostasis and barrier function. Comprehensive analyses of its function would substantially benefit from a catalog of reference genes derived from metagenomic sequencing. The existing catalog for the human skin microbiome is based on samples from limited individuals from a single cohort on reference genomes, which limits the coverage of global skin microbiome diversity. Results: In the present study, we have used shotgun metagenomics to newly sequence 822 skin samples from Han Chinese, which were subsequently combined with 538 previously sequenced North American samples to construct an integrated Human Skin Microbial Gene Catalog (iHSMGC). The iHSMGC comprised 10,930,638 genes with the detection of 4,879,024 new genes. Characterization of the human skin resistome based on iHSMGC confirmed that skin commensals, such as Staphylococcus spp, are an important reservoir of antibiotic resistance genes (ARGs). Further analyses of skin microbial ARGs detected microbe-specific and skin site-specific ARG signatures. -
Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341 -
Evaluation of MALDI Biotyper for Identification of Taylorella Equigenitalis and Taylorella Asinigenitalis Kristina Lantz Iowa State University
Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2017 Evaluation of MALDI Biotyper for identification of Taylorella equigenitalis and Taylorella asinigenitalis Kristina Lantz Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Microbiology Commons, and the Veterinary Medicine Commons Recommended Citation Lantz, Kristina, "Evaluation of MALDI Biotyper for identification of Taylorella equigenitalis and Taylorella asinigenitalis" (2017). Graduate Theses and Dissertations. 16520. https://lib.dr.iastate.edu/etd/16520 This Thesis is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Evaluation of MALDI Biotyper for identification of Taylorella equigenitalis and Taylorella asinigenitalis by Kristina Lantz A thesis submitted to the graduate faculty in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Major: Veterinary Microbiology Program of Study Committee: Ronald Griffith, Major Professor Steve Carlson Matthew Erdman Timothy Frana The student author and the program of study committee are solely responsible for the content of this thesis. The Graduate College will ensure this thesis is globally accessible and will not permit -
Fish Bacterial Flora Identification Via Rapid Cellular Fatty Acid Analysis
Fish bacterial flora identification via rapid cellular fatty acid analysis Item Type Thesis Authors Morey, Amit Download date 09/10/2021 08:41:29 Link to Item http://hdl.handle.net/11122/4939 FISH BACTERIAL FLORA IDENTIFICATION VIA RAPID CELLULAR FATTY ACID ANALYSIS By Amit Morey /V RECOMMENDED: $ Advisory Committe/ Chair < r Head, Interdisciplinary iProgram in Seafood Science and Nutrition /-■ x ? APPROVED: Dean, SchooLof Fisheries and Ocfcan Sciences de3n of the Graduate School Date FISH BACTERIAL FLORA IDENTIFICATION VIA RAPID CELLULAR FATTY ACID ANALYSIS A THESIS Presented to the Faculty of the University of Alaska Fairbanks in Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCE By Amit Morey, M.F.Sc. Fairbanks, Alaska h r A Q t ■ ^% 0 /v AlA s ((0 August 2007 ^>c0^b Abstract Seafood quality can be assessed by determining the bacterial load and flora composition, although classical taxonomic methods are time-consuming and subjective to interpretation bias. A two-prong approach was used to assess a commercially available microbial identification system: confirmation of known cultures and fish spoilage experiments to isolate unknowns for identification. Bacterial isolates from the Fishery Industrial Technology Center Culture Collection (FITCCC) and the American Type Culture Collection (ATCC) were used to test the identification ability of the Sherlock Microbial Identification System (MIS). Twelve ATCC and 21 FITCCC strains were identified to species with the exception of Pseudomonas fluorescens and P. putida which could not be distinguished by cellular fatty acid analysis. The bacterial flora changes that occurred in iced Alaska pink salmon ( Oncorhynchus gorbuscha) were determined by the rapid method. -
Assessing the Temporal Dynamics of the Lower Urinary Tract Microbiota and the Effects of Lifestyle
Loyola University Chicago Loyola eCommons Dissertations Theses and Dissertations 2019 Assessing the Temporal Dynamics of the Lower Urinary Tract Microbiota and the Effects of Lifestyle Travis Kyle Price Follow this and additional works at: https://ecommons.luc.edu/luc_diss Part of the Microbiology Commons Recommended Citation Price, Travis Kyle, "Assessing the Temporal Dynamics of the Lower Urinary Tract Microbiota and the Effects of Lifestyle" (2019). Dissertations. 3367. https://ecommons.luc.edu/luc_diss/3367 This Dissertation is brought to you for free and open access by the Theses and Dissertations at Loyola eCommons. It has been accepted for inclusion in Dissertations by an authorized administrator of Loyola eCommons. For more information, please contact [email protected]. This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License. Copyright © 2019 Travis Kyle Price LOYOLA UNIVERSITY CHICAGO ASSESSING THE TEMPORAL DYNAMICS OF THE LOWER URINARY TRACT MICROBIOTA AND THE EFFECTS OF LIFESTYLE A DISSERTATION SUBMITTED TO THE FACULTY OF THE GRADUATE SCHOOL IN CANDIDACY FOR THE DEGREE OF DOCTOR OF PHILOSOPHY PROGRAM IN MICROBIOLOGY AND IMMUNOLOGY BY TRAVIS KYLE PRICE CHICAGO, IL MAY 2019 i Copyright by Travis Kyle Price, 2019 All Rights Reserved ii ACKNOWLEDGMENTS I would like to thank everyone that made this thesis possible. First and foremost, I want to thank Dr. Alan Wolfe. I could not have asked for a better mentor. I don’t think there will ever be another period of my life where I grow as a scientist, as a professional, or as a person more than I did under your mentorship. -
Standoff Detection and Classification of Bacteria by Multispectral Laser-Induced Fluorescence
Adv. Opt. Techn. 2017; 6(2): 75–83 Research Article Open Access Frank Duschek*, Lea Fellner, Florian Gebert, Karin Grünewald, Anja Köhntopp, Marian Kraus, Peter Mahnke, Carsten Pargmann, Herbert Tomaso and Arne Walter Standoff detection and classification of bacteria by multispectral laser-induced fluorescence DOI 10.1515/aot-2016-0066 OCIS codes: 160.1435; 280.1415; 300.2530; 280.0280; Received December 2, 2016; accepted February 6, 2017; previously 000.3860. published online March 31, 2017 Abstract: Biological hazardous substances such as cer- tain fungi and bacteria represent a high risk for the broad 1 Introduction public if fallen into wrong hands. Incidents based on Hazardous bacteria represent a major threat to modern bio-agents are commonly considered to have unpredict- societies if released into the environment. Aerosols of bac- able and complex consequences for first responders and teria can occur naturally when infected animals or humans people. The impact of such an event can be minimized spread a pathogen, but they can also be released by acci- by an early and fast detection of hazards. The presented dents and as a terrorist attack. Once people are infected, approach is based on optical standoff detection apply- bacteria may easily spread aided by the fact that their detri- ing laser-induced fluorescence (LIF) on bacteria. The LIF mental effects can occur with a certain time delay. Therefore, bio-detector has been designed for outdoor operation fast and reliable detection and identification of bacteria is at standoff distances from 20 m up to more than 100 m. essential for the containment and the decontamination of The detector acquires LIF spectral data for two different affected areas and people. -
Tracking Reservoirs of Antimicrobial Resistance Genes in a Complex Microbial Community Using Metagenomic Hi-C: the Case of Bovine Digital Dermatitis
antibiotics Article Tracking Reservoirs of Antimicrobial Resistance Genes in a Complex Microbial Community Using Metagenomic Hi-C: The Case of Bovine Digital Dermatitis Ashenafi F. Beyi 1 , Alan Hassall 2, Gregory J. Phillips 1 and Paul J. Plummer 1,2,3,* 1 Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA; [email protected] (A.F.B.); [email protected] (G.J.P.) 2 Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA 50011, USA; [email protected] 3 National Institute of Antimicrobial Resistance Research and Education, Ames, IA 50010, USA * Correspondence: [email protected] Abstract: Bovine digital dermatitis (DD) is a contagious infectious cause of lameness in cattle with unknown definitive etiologies. Many of the bacterial species detected in metagenomic analyses of DD lesions are difficult to culture, and their antimicrobial resistance status is largely unknown. Recently, a novel proximity ligation-guided metagenomic approach (Hi-C ProxiMeta) has been used to identify bacterial reservoirs of antimicrobial resistance genes (ARGs) directly from microbial communities, without the need to culture individual bacteria. The objective of this study was to track tetracycline resistance determinants in bacteria involved in DD pathogenesis using Hi-C. A pooled sample of macerated tissues from clinical DD lesions was used for this purpose. Metagenome deconvolution Citation: Beyi, A.F.; Hassall, A.; ≥ Phillips, G.J.; Plummer, P.J. Tracking using ProxiMeta resulted in the creation of 40 metagenome-assembled genomes with 80% complete Reservoirs of Antimicrobial genomes, classified into five phyla. Further, 1959 tetracycline resistance genes and ARGs conferring Resistance Genes in a Complex resistance to aminoglycoside, beta-lactams, sulfonamide, phenicol, lincosamide, and erythromycin Microbial Community Using were identified along with their bacterial hosts. -
And Gastrointestinal Disturbances Samples from Children with Autism
Downloaded from Application of Novel PCR-Based mbio.asm.org Methods for Detection, Quantitation, and Phylogenetic Characterization of Sutterella Species in Intestinal Biopsy on January 10, 2012 - Published by Samples from Children with Autism and Gastrointestinal Disturbances Brent L. Williams, Mady Hornig, Tanmay Parekh, et al. 2012. Application of Novel PCR-Based Methods for Detection, Quantitation, and Phylogenetic Characterization of Sutterella Species in Intestinal Biopsy Samples from Children with Autism and Gastrointestinal Disturbances . mBio 3(1): . doi:10.1128/mBio.00261-11. mbio.asm.org Updated information and services can be found at: http://mbio.asm.org/content/3/1/e00261-11.full.html SUPPLEMENTAL http://mbio.asm.org/content/3/1/e00261-11.full.html#SUPPLEMENTAL MATERIAL REFERENCES This article cites 43 articles, 23 of which can be accessed free at: http://mbio.asm.org/content/3/1/e00261-11.full.html#ref-list-1 CONTENT ALERTS Receive: RSS Feeds, eTOCs, free email alerts (when new articles cite this article), more>> Information about commercial reprint orders: http://mbio.asm.org/misc/reprints.xhtml Information about Print on Demand and other content delivery options: http://mbio.asm.org/misc/contentdelivery.xhtml To subscribe to another ASM Journal go to: http://journals.asm.org/subscriptions/ Downloaded from RESEARCH ARTICLE Application of Novel PCR-Based Methods for Detection, Quantitation, mbio.asm.org and Phylogenetic Characterization of Sutterella Species in Intestinal Biopsy Samples from Children with Autism and Gastrointestinal on January 10, 2012 - Published by Disturbances Brent L. Williams, Mady Hornig, Tanmay Parekh, and W. Ian Lipkin Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA ABSTRACT Gastrointestinal disturbances are commonly reported in children with autism and may be associated with composi- tional changes in intestinal bacteria. -
Metabolic Roles of Uncultivated Bacterioplankton Lineages in the Northern Gulf of Mexico 2 “Dead Zone” 3 4 J
bioRxiv preprint doi: https://doi.org/10.1101/095471; this version posted June 12, 2017. 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. 1 Metabolic roles of uncultivated bacterioplankton lineages in the northern Gulf of Mexico 2 “Dead Zone” 3 4 J. Cameron Thrash1*, Kiley W. Seitz2, Brett J. Baker2*, Ben Temperton3, Lauren E. Gillies4, 5 Nancy N. Rabalais5,6, Bernard Henrissat7,8,9, and Olivia U. Mason4 6 7 8 1. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA 9 2. Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port 10 Aransas, TX, USA 11 3. School of Biosciences, University of Exeter, Exeter, UK 12 4. Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, 13 FL, USA 14 5. Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, 15 LA, USA 16 6. Louisiana Universities Marine Consortium, Chauvin, LA USA 17 7. Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 18 13288 Marseille, France 19 8. INRA, USC 1408 AFMB, F-13288 Marseille, France 20 9. Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia 21 22 *Correspondence: 23 JCT [email protected] 24 BJB [email protected] 25 26 27 28 Running title: Decoding microbes of the Dead Zone 29 30 31 Abstract word count: 250 32 Text word count: XXXX 33 34 Page 1 of 31 bioRxiv preprint doi: https://doi.org/10.1101/095471; this version posted June 12, 2017. -
A Genomic Perspective on a New Bacterial Genus and Species From
Whiteson et al. BMC Genomics 2014, 15:169 http://www.biomedcentral.com/1471-2164/15/169 RESEARCH ARTICLE Open Access A genomic perspective on a new bacterial genus and species from the Alcaligenaceae family, Basilea psittacipulmonis Katrine L Whiteson1,5*, David Hernandez1, Vladimir Lazarevic1, Nadia Gaia1, Laurent Farinelli2, Patrice François1, Paola Pilo3, Joachim Frey3 and Jacques Schrenzel1,4 Abstract Background: A novel Gram-negative, non-haemolytic, non-motile, rod-shaped bacterium was discovered in the lungs of a dead parakeet (Melopsittacus undulatus) that was kept in captivity in a petshop in Basel, Switzerland. The organism is described with a chemotaxonomic profile and the nearly complete genome sequence obtained through the assembly of short sequence reads. Results: Genome sequence analysis and characterization of respiratory quinones, fatty acids, polar lipids, and biochemical phenotype is presented here. Comparison of gene sequences revealed that the most similar species is Pelistega europaea, with BLAST identities of only 93% to the 16S rDNA gene, 76% identity to the rpoB gene, and a similar GC content (~43%) as the organism isolated from the parakeet, DSM 24701 (40%). The closest full genome sequences are those of Bordetella spp. and Taylorella spp. High-throughput sequencing reads from the Illumina-Solexa platform were assembled with the Edena de novo assembler to form 195 contigs comprising the ~2 Mb genome. Genome annotation with RAST, construction of phylogenetic trees with the 16S rDNA (rrs) gene sequence and the rpoB gene, and phylogenetic placement using other highly conserved marker genes with ML Tree all suggest that the bacterial species belongs to the Alcaligenaceae family. -
Ribosomal Ribonucleic Acid Cistron Similarities and Deoxyribonucleic Acid Homologies of Neisseria , Kingella , Eikenella, Simons
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Apr. 1989, p. 185-198 Vol. 39, No. 2 0020-7713/89/020185-14$02.0010 Copyright 0 1989, International Union of Microbiological Societies Ribosomal Ribonucleic Acid Cistron Similarities and Deoxyribonucleic Acid Homologies of Neisseria , Kingella , Eikenella, Simonsiella, Alysiella, and Centers for Disease Control Groups EF-4 and M-5 in the Emended Family Neisseriaceae R. ROSSAU,ll- G. VANDENBUSSCHE,l S. THIELEMANS,l P. SEGERS,l H. GROSCH,2 E. GOTHE,2 W. MANNHEIM,2 AND J. DE LEY1* Laboratorium voor Microbiologie en microbiele Genetica, Rijksuniversiteit, Ledeganckstraat 35, B-9000 Gent, Belgium,' and Zentrum fur Hygiene und medizinische Mikrobiologie, Klinikum der Philipps- Universitat, 0-3550Marburg-Lahn, Federal Republic of Germany2 We detected distinct taxonomic relationships among the true Neisseria species, Kingella kingae, Kingella denitrGcans, Eikenella corrodens, all Simonsiella species, the type strain of Alysiellafiliformis, and members of Centers for Disease Control groups EF-4 and M-5. All these taxa constitute one large separate cluster having high levels of ribosomal ribonucleic acid cistron similarity (thermal denaturation temperature range, 74 to 81°C) in ribosomal ribonucleic acid superfamily 111. There are at least four subbranches. We found high deoxyribonucleic acid (DNA)-DNA homology values between Neisseria gonorrhoeae and some other true Neisseriu species and within the following species: Simonsiella muelleri, Simonsiella crassa, Simonsiella steedue, Kingella denitrificans, and Eikenella corrodens. All of the members of this large cluster have genome base compositions in the range from 42.8 to 57.7 mol% guanine plus cytosine. The molecular complexities of the genomic DNAs are 2.2 X lo9 to 2.7 x lo9 for Sirnonsiella and Alysiella species and 1.4 X lo9 to 1.8 X lo9 for the other members of this large cluster. -
Development of a PCR-Based Method for Monitoring the Status of Alcaligenes Species in the Agricultural Environment
Biocontrol Science, 2014, Vol. 19, No. 1, 23－31 Original Development of a PCR-Based Method for Monitoring the Status of Alcaligenes Species in the Agricultural Environment MIYO NAKANO1, MASUMI NIWA2, AND NORIHIRO NISHIMURA1＊ 1 Department of Translational Medical Science and Molecular and Cellular Pharmacology, Pharmacogenomics, and Pharmacoinformatics, Mie University Graduate School of Medicine, Mie University, 2-174 Edobashi, Tsu, Mie 514-8507, Japan 2 DESIGNER FOODS. Co., Ltd. NALIC207, Chikusa 2-22-8, Chikusa-ku, Nagoya, Aichi 464-0858, Japan Received 1 April, 2013/Accepted 14 September, 2013 To analyze the status of the genus Alcaligenes in the agricultural environment, we developed a PCR method for detection of these species from vegetables and farming soil. The selected PCR primers amplified a 107-bp fragment of the 16S rRNA gene in a specific PCR assay with a detection limit of 1.06 pg of pure culture DNA, corresponding to DNA extracted from approxi- mately 23 cells of Alcaligenes faecalis. Meanwhile, PCR primers generated a detectable amount of the amplicon from 2.2×102 CFU/ml cell suspensions from the soil. Analysis of vegetable phyl- loepiphytic and farming soil microbes showed that bacterial species belonging to the genus Alcaligenes were present in the range from 0.9×100 CFU per gram（ or cm2）（ Japanese radish: Raphanus sativus var. longipinnatus） to more than 1.1×104 CFU/g（ broccoli flowers: Brassica oleracea var. italic）, while 2.4×102 to 4.4×103 CFU/g were detected from all soil samples. These results indicated that Alcaligenes species are present in the phytosphere at levels 10–1000 times lower than those in soil.