Organisms and Pathogens Quiz by Laura King, MA, ELS
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Chemical Structures of Some Examples of Earlier Characterized Antibiotic and Anticancer Specialized
Supplementary figure S1: Chemical structures of some examples of earlier characterized antibiotic and anticancer specialized metabolites: (A) salinilactam, (B) lactocillin, (C) streptochlorin, (D) abyssomicin C and (E) salinosporamide K. Figure S2. Heat map representing hierarchical classification of the SMGCs detected in all the metagenomes in the dataset. Table S1: The sampling locations of each of the sites in the dataset. Sample Sample Bio-project Site depth accession accession Samples Latitude Longitude Site description (m) number in SRA number in SRA AT0050m01B1-4C1 SRS598124 PRJNA193416 Atlantis II water column 50, 200, Water column AT0200m01C1-4D1 SRS598125 21°36'19.0" 38°12'09.0 700 and above the brine N "E (ATII 50, ATII 200, 1500 pool water layers AT0700m01C1-3D1 SRS598128 ATII 700, ATII 1500) AT1500m01B1-3C1 SRS598129 ATBRUCL SRS1029632 PRJNA193416 Atlantis II brine 21°36'19.0" 38°12'09.0 1996– Brine pool water ATBRLCL1-3 SRS1029579 (ATII UCL, ATII INF, N "E 2025 layers ATII LCL) ATBRINP SRS481323 PRJNA219363 ATIID-1a SRS1120041 PRJNA299097 ATIID-1b SRS1120130 ATIID-2 SRS1120133 2168 + Sea sediments Atlantis II - sediments 21°36'19.0" 38°12'09.0 ~3.5 core underlying ATII ATIID-3 SRS1120134 (ATII SDM) N "E length brine pool ATIID-4 SRS1120135 ATIID-5 SRS1120142 ATIID-6 SRS1120143 Discovery Deep brine DDBRINP SRS481325 PRJNA219363 21°17'11.0" 38°17'14.0 2026– Brine pool water N "E 2042 layers (DD INF, DD BR) DDBRINE DD-1 SRS1120158 PRJNA299097 DD-2 SRS1120203 DD-3 SRS1120205 Discovery Deep 2180 + Sea sediments sediments 21°17'11.0" -
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. -
Bartonella Apis Sp. Nov., a Honey Bee Gut Symbiont of the Class Alphaproteobacteria
Serveur Academique´ Lausannois SERVAL serval.unil.ch Author Manuscript Faculty of Biology and Medicine Publication This paper has been peer-reviewed but does not include the final publisher proof-corrections or journal pagination. Published in final edited form as: Title: Bartonella apis sp. nov., a honey bee gut symbiont of the class Alphaproteobacteria. Authors: Keˇsnerov´aL, Moritz R, Engel P Journal: International journal of systematic and evolutionary microbiology Year: 2016 Jan Issue: 66 Volume: 1 Pages: 414-21 DOI: 10.1099/ijsem.0.000736 In the absence of a copyright statement, users should assume that standard copyright protection applies, unless the article contains an explicit statement to the contrary. In case of doubt, contact the journal publisher to verify the copyright status of an article. 1 Bartonella apis sp. nov., a honey bee gut symbiont of the 2 class Alphaproteobacteria 3 4 Lucie Kešnerová, Roxane Moritz, Philipp Engel* 5 6 Department of Fundamental Microbiology, University of Lausanne, CH-1015 7 Lausanne, Switzerland 8 9 Running title: Description of a bee gut symbiont 10 11 *Correspondence: 12 Prof. Philipp Engel 13 Department of Fundamental Microbiology 14 University of Lausanne, CH-1015 Lausanne, Switzerland 15 Tel.: +41 (0)21 692 56 12 16 e-mail: [email protected] 17 18 Category: New Taxa – Proteobacteria 19 Keywords: Apis mellifera; insect; Bartonella; gut microbiota; Alpha-1 20 21 Sequence deposition: The 16S rRNA gene sequences and protein-coding gene 22 sequences of the bacterial strains PEB0122T, PEB0149, PEB0150, BBC0104, and 23 BBC0108 from Apis mellifera, and the uncultured Rhizobiales bacterium from 24 Herpagnathos saltator are deposited in GenBank with accession numbers KP987849 25 – KP987886 and KT315729 – KT315734. -
View Tickborne Diseases Sample Report
1360 Bayport Ave, Ste B. San Carlos, CA 94070 1(866) 364-0963 | [email protected] | www. vibrant-wellness.com PATIENT PROVIDER NAME: DEMO REPORT GENDER: Male PRACTICE NAME: Vibrant IT4 Practice DATE OF BIRTH: 04/14/1998 AGE: 22 PROVIDER NAME: Demo Client, DDD (999994) ADDRESS: TEST STREET, TEST CITY, KY- 42437. ACCESSION ID: 2009220006 PHLEBOTOMIST: 607 SPECIMEN COLLECTION TIME: 09-21-2020 11:14 SPECIMEN RECEIVED TIME: 09-22-2020 05:14 FINAL REPORT TIME: 09-25-2020 15:56 FASTING: FASTING Your Vibrant Wellness TickBorne 2.0 panel results are enclosed. These results are intended to aid in the diagnosis of tickborne diseases by your healthcare provider. The Vibrant Tickborne Diseases panel tests for IgG and IgM antibodies for Borreliosis/Lyme disease as well as co-infection(s) and opportunistic infections with other tick-borne illnesses along with detection of DNA of the species causing these infections. The Vibrant Immunochip test is a semiquantitative assay that detects IgG and IgM antibodies in human serum. The PCR Test is a real-time PCR Assay designed for qualitative detection of infectious group- specific DNA in clinical samples. Interpretation of Report: The test results of antibody levels to the individual antigens are calculated by comparing the average intensity of the individual antibody to that of a reference population and cut-off chosen for each protein. Reference ranges have been established using a well characterized set of more than 300 serum samples and antibodies to specific bacteria tested. The results are displayed as In Control, Moderate, or High Risk.for each antigen tested. -
Genetic Diversity of Bartonella Species in Small Mammals in the Qaidam
www.nature.com/scientificreports OPEN Genetic diversity of Bartonella species in small mammals in the Qaidam Basin, western China Huaxiang Rao1, Shoujiang Li3, Liang Lu4, Rong Wang3, Xiuping Song4, Kai Sun5, Yan Shi3, Dongmei Li4* & Juan Yu2* Investigation of the prevalence and diversity of Bartonella infections in small mammals in the Qaidam Basin, western China, could provide a scientifc basis for the control and prevention of Bartonella infections in humans. Accordingly, in this study, small mammals were captured using snap traps in Wulan County and Ge’ermu City, Qaidam Basin, China. Spleen and brain tissues were collected and cultured to isolate Bartonella strains. The suspected positive colonies were detected with polymerase chain reaction amplifcation and sequencing of gltA, ftsZ, RNA polymerase beta subunit (rpoB) and ribC genes. Among 101 small mammals, 39 were positive for Bartonella, with the infection rate of 38.61%. The infection rate in diferent tissues (spleens and brains) (χ2 = 0.112, P = 0.738) and gender (χ2 = 1.927, P = 0.165) of small mammals did not have statistical diference, but that in diferent habitats had statistical diference (χ2 = 10.361, P = 0.016). Through genetic evolution analysis, 40 Bartonella strains were identifed (two diferent Bartonella species were detected in one small mammal), including B. grahamii (30), B. jaculi (3), B. krasnovii (3) and Candidatus B. gerbillinarum (4), which showed rodent-specifc characteristics. B. grahamii was the dominant epidemic strain (accounted for 75.0%). Furthermore, phylogenetic analysis showed that B. grahamii in the Qaidam Basin, might be close to the strains isolated from Japan and China. -
“Candidatus Deianiraea Vastatrix” with the Ciliate Paramecium Suggests
bioRxiv preprint doi: https://doi.org/10.1101/479196; this version posted November 27, 2018. 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-ND 4.0 International license. The extracellular association of the bacterium “Candidatus Deianiraea vastatrix” with the ciliate Paramecium suggests an alternative scenario for the evolution of Rickettsiales 5 Castelli M.1, Sabaneyeva E.2, Lanzoni O.3, Lebedeva N.4, Floriano A.M.5, Gaiarsa S.5,6, Benken K.7, Modeo L. 3, Bandi C.1, Potekhin A.8, Sassera D.5*, Petroni G.3* 1. Centro Romeo ed Enrica Invernizzi Ricerca Pediatrica, Dipartimento di Bioscienze, Università 10 degli studi di Milano, Milan, Italy 2. Department of Cytology and Histology, Faculty of Biology, Saint Petersburg State University, Saint-Petersburg, Russia 3. Dipartimento di Biologia, Università di Pisa, Pisa, Italy 4 Centre of Core Facilities “Culture Collections of Microorganisms”, Saint Petersburg State 15 University, Saint Petersburg, Russia 5. Dipartimento di Biologia e Biotecnologie, Università degli studi di Pavia, Pavia, Italy 6. UOC Microbiologia e Virologia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy 7. Core Facility Center for Microscopy and Microanalysis, Saint Petersburg State University, Saint- Petersburg, Russia 20 8. Department of Microbiology, Faculty of Biology, Saint Petersburg State University, Saint- Petersburg, Russia * Corresponding authors, contacts: [email protected] ; [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/479196; this version posted November 27, 2018. -
Ehrlichiosis and Anaplasmosis Are Tick-Borne Diseases Caused by Obligate Anaplasmosis: Intracellular Bacteria in the Genera Ehrlichia and Anaplasma
Ehrlichiosis and Importance Ehrlichiosis and anaplasmosis are tick-borne diseases caused by obligate Anaplasmosis: intracellular bacteria in the genera Ehrlichia and Anaplasma. These organisms are widespread in nature; the reservoir hosts include numerous wild animals, as well as Zoonotic Species some domesticated species. For many years, Ehrlichia and Anaplasma species have been known to cause illness in pets and livestock. The consequences of exposure vary Canine Monocytic Ehrlichiosis, from asymptomatic infections to severe, potentially fatal illness. Some organisms Canine Hemorrhagic Fever, have also been recognized as human pathogens since the 1980s and 1990s. Tropical Canine Pancytopenia, Etiology Tracker Dog Disease, Ehrlichiosis and anaplasmosis are caused by members of the genera Ehrlichia Canine Tick Typhus, and Anaplasma, respectively. Both genera contain small, pleomorphic, Gram negative, Nairobi Bleeding Disorder, obligate intracellular organisms, and belong to the family Anaplasmataceae, order Canine Granulocytic Ehrlichiosis, Rickettsiales. They are classified as α-proteobacteria. A number of Ehrlichia and Canine Granulocytic Anaplasmosis, Anaplasma species affect animals. A limited number of these organisms have also Equine Granulocytic Ehrlichiosis, been identified in people. Equine Granulocytic Anaplasmosis, Recent changes in taxonomy can make the nomenclature of the Anaplasmataceae Tick-borne Fever, and their diseases somewhat confusing. At one time, ehrlichiosis was a group of Pasture Fever, diseases caused by organisms that mostly replicated in membrane-bound cytoplasmic Human Monocytic Ehrlichiosis, vacuoles of leukocytes, and belonged to the genus Ehrlichia, tribe Ehrlichieae and Human Granulocytic Anaplasmosis, family Rickettsiaceae. The names of the diseases were often based on the host Human Granulocytic Ehrlichiosis, species, together with type of leukocyte most often infected. -
Bartonella Henselae • Fleas and Black-Legged Ticks (Also Called Deer Ticks) of the Genus Ixodes May Serve As Vectors, but This Has Not Disease Agent: Been Proven
APPENDIX 2 Bartonella henselae • Fleas and black-legged ticks (also called deer ticks) of the genus Ixodes may serve as vectors, but this has not Disease Agent: been proven. • Bartonella henselae Blood Phase: Disease Agent Characteristics: • Agent found in endothelial cells and associated with RBCs in symptomatic cases • Gram-negative bacillus or coccobacillus, aerobic, • Occult bacteremia sometimes occurs in the absence nonmotile, nonspore-forming, facultatively intracel- of specific antibodies. lular bacterium • Order: Rhizobiales; Family: Bartonellaceae Survival/Persistence in Blood Products: • Size: 0.3-0.6 ¥ 0.3-1.0 mm • Nucleic acid: Approximately 1900 kb of DNA • A spiking study suggests that B. henselae added to RBCs can be recovered on solid media through 35 Disease Name: days of storage at 4°C. • Cat scratch disease • Cat scratch fever Transmission by Blood Transfusion: • Bacillary angiomatosis • Theoretical • Bacillary peliosis Cases/Frequency in Population: Priority Level: • 22,000 cases per year estimated in the US • Scientific/Epidemiologic evidence regarding blood • 2-6% in US blood donors safety: Theoretical • Cumulative seroprevalence of 7.1% to B. henselae and • Public perception and/or regulatory concern regard- B. quintana in US veterinary professionals ing blood safety: Absent • Public concern regarding disease agent: Very low Incubation Period: Background: • 3-10 days to appearance of papule at inoculation site; regional adenopathy may follow after a few weeks • In 1909,ALBartondescribed organisms that adhered to RBCs. Likelihood of Clinical Disease: • The name Bartonella bacilliformis was used for the • Relatively benign and self-limiting, lasting 6-12 weeks only member of the group identified before 1993. in the absence of antibiotic therapy • Several other species of Bartonella are known to infect humans, but at present, B. -
Table S4. Phylogenetic Distribution of Bacterial and Archaea Genomes in Groups A, B, C, D, and X
Table S4. Phylogenetic distribution of bacterial and archaea genomes in groups A, B, C, D, and X. Group A a: Total number of genomes in the taxon b: Number of group A genomes in the taxon c: Percentage of group A genomes in the taxon a b c cellular organisms 5007 2974 59.4 |__ Bacteria 4769 2935 61.5 | |__ Proteobacteria 1854 1570 84.7 | | |__ Gammaproteobacteria 711 631 88.7 | | | |__ Enterobacterales 112 97 86.6 | | | | |__ Enterobacteriaceae 41 32 78.0 | | | | | |__ unclassified Enterobacteriaceae 13 7 53.8 | | | | |__ Erwiniaceae 30 28 93.3 | | | | | |__ Erwinia 10 10 100.0 | | | | | |__ Buchnera 8 8 100.0 | | | | | | |__ Buchnera aphidicola 8 8 100.0 | | | | | |__ Pantoea 8 8 100.0 | | | | |__ Yersiniaceae 14 14 100.0 | | | | | |__ Serratia 8 8 100.0 | | | | |__ Morganellaceae 13 10 76.9 | | | | |__ Pectobacteriaceae 8 8 100.0 | | | |__ Alteromonadales 94 94 100.0 | | | | |__ Alteromonadaceae 34 34 100.0 | | | | | |__ Marinobacter 12 12 100.0 | | | | |__ Shewanellaceae 17 17 100.0 | | | | | |__ Shewanella 17 17 100.0 | | | | |__ Pseudoalteromonadaceae 16 16 100.0 | | | | | |__ Pseudoalteromonas 15 15 100.0 | | | | |__ Idiomarinaceae 9 9 100.0 | | | | | |__ Idiomarina 9 9 100.0 | | | | |__ Colwelliaceae 6 6 100.0 | | | |__ Pseudomonadales 81 81 100.0 | | | | |__ Moraxellaceae 41 41 100.0 | | | | | |__ Acinetobacter 25 25 100.0 | | | | | |__ Psychrobacter 8 8 100.0 | | | | | |__ Moraxella 6 6 100.0 | | | | |__ Pseudomonadaceae 40 40 100.0 | | | | | |__ Pseudomonas 38 38 100.0 | | | |__ Oceanospirillales 73 72 98.6 | | | | |__ Oceanospirillaceae -
Bartonella Henselae Detected in Malignant Melanoma, a Preliminary Study
pathogens Article Bartonella henselae Detected in Malignant Melanoma, a Preliminary Study Marna E. Ericson 1, Edward B. Breitschwerdt 2 , Paul Reicherter 3, Cole Maxwell 4, Ricardo G. Maggi 2, Richard G. Melvin 5 , Azar H. Maluki 4,6 , Julie M. Bradley 2, Jennifer C. Miller 7, Glenn E. Simmons, Jr. 5 , Jamie Dencklau 4, Keaton Joppru 5, Jack Peterson 4, Will Bae 4, Janet Scanlon 4 and Lynne T. Bemis 5,* 1 T Lab Inc., 910 Clopper Road, Suite 220S, Gaithersburg, MD 20878, USA; [email protected] 2 Intracellular Pathogens Research Laboratory, Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA; [email protected] (E.B.B.); [email protected] (R.G.M.); [email protected] (J.M.B.) 3 Dermatology Clinic, Truman Medical Center, University of Missouri, Kansas City, MO 64108, USA; [email protected] 4 Department of Dermatology, University of Minnesota, Minneapolis, MN 55455, USA; [email protected] (C.M.); [email protected] (A.H.M.); [email protected] (J.D.); [email protected] (J.P.); [email protected] (W.B.); [email protected] (J.S.) 5 Department of Biomedical Sciences, Duluth Campus, Medical School, University of Minnesota, Duluth, MN 55812, USA; [email protected] (R.G.M.); [email protected] (G.E.S.J.); [email protected] (K.J.) 6 Department of Dermatology, College of Medicine, University of Kufa, Kufa 54003, Iraq 7 Galaxy Diagnostics Inc., Research Triangle Park, NC 27709, USA; [email protected] Citation: Ericson, M.E.; * Correspondence: [email protected]; Tel.: +1-720-560-0278; Fax: +1-218-726-7906 Breitschwerdt, E.B.; Reicherter, P.; Maxwell, C.; Maggi, R.G.; Melvin, Abstract: Bartonella bacilliformis (B. -
Gene Gain and Loss Events in Rickettsia and Orientia Species Kalliopi Georgiades1,2, Vicky Merhej1, Khalid El Karkouri1, Didier Raoult1, Pierre Pontarotti2*
Georgiades et al. Biology Direct 2011, 6:6 http://www.biology-direct.com/content/6/1/6 RESEARCH Open Access Gene gain and loss events in Rickettsia and Orientia species Kalliopi Georgiades1,2, Vicky Merhej1, Khalid El Karkouri1, Didier Raoult1, Pierre Pontarotti2* Abstract Background: Genome degradation is an ongoing process in all members of the Rickettsiales order, which makes these bacterial species an excellent model for studying reductive evolution through interspecies variation in genome size and gene content. In this study, we evaluated the degree to which gene loss shaped the content of some Rickettsiales genomes. We shed light on the role played by horizontal gene transfers in the genome evolution of Rickettsiales. Results: Our phylogenomic tree, based on whole-genome content, presented a topology distinct from that of the whole core gene concatenated phylogenetic tree, suggesting that the gene repertoires involved have different evolutionary histories. Indeed, we present evidence for 3 possible horizontal gene transfer events from various organisms to Orientia and 6 to Rickettsia spp., while we also identified 3 possible horizontal gene transfer events from Rickettsia and Orientia to other bacteria. We found 17 putative genes in Rickettsia spp. that are probably the result of de novo gene creation; 2 of these genes appear to be functional. On the basis of these results, we were able to reconstruct the gene repertoires of “proto-Rickettsiales” and “proto-Rickettsiaceae”, which correspond to the ancestors of Rickettsiales and Rickettsiaceae, respectively. Finally, we found that 2,135 genes were lost during the evolution of the Rickettsiaceae to an intracellular lifestyle. Conclusions: Our phylogenetic analysis allowed us to track the gene gain and loss events occurring in bacterial genomes during their evolution from a free-living to an intracellular lifestyle. -
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