DOCSLIB.ORG

Hill Submission 2

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Hill Submission 2 MMeettaaggeennoommiicc aannaallyysseess rreevveeaall aannttiibbiioottiicc--iinndduucceedd tteemmppoorraall aanndd ssppaattiiaall cchhaannggeess iinn iinntteessttiinnaall mmiiccrroobbiioottaa wwiitthh aassssoocciiaatteedd aalltteerraattiioonnss iinn iimmmmuunnee hhoommeeoossttaassiiss David A. Hilla, Christian Hoffmannb, Michael C. Abta, Yurong Dua, Thomas J. Kirna, Frederic D. Bushmanb, David Artisa aDept. of Pathobiology, bDept. of Microbiology, University of Pennsylvania, Philadelphia, PA 19104 Results Figure 4. Antibiotics alter stool bacterial communities over 1 9 y y a a D D time. c c d i i t t Abstract e e n o o u u i i l l A e B b b a a i i g Figure 1. Antibiotic administration mimics molecular, t t v v e n - n - L H2O ABX Phyl—um————————————Cl—as—s-—Or—de—r———————Family-Genus Antibiotic Day 0 A P A P Despite widespread use of antibiotics, few studies have measured their effects 100% Verrucomicrobi—a ——————Verrucomicrobiae-V—er—ruc—o—mi—cro—b—ial—es————————————Verrucomicrobiaceae-Akkermansia 0.0 6.1 0.015 anatomic, histologic, and immunologic characteristics of T—M7———————TM7 genera incertae sedis-Un—kn—ow—n———————————————————Unknown-Unknown 0.6 0.0 0.007 0.0 0.015 ————————Gammaproteobacteria-E—nte—ro—ba—c—ter—ial—es—————————————Enterobacteriaceae-Enterobacter on the burden or diversity of bacterial communities in the mammalian intestine. 90% Proteobact—eri—a-———————Betaproteobacteria-Burkholderial—es———————————————————Unknown-Unknown ———————————Alphaproteobacteria-Unknow—n———————————————————Unknown-Unknown reduced microbial stimulation. —————————E—ry—sip—e—lot—ric—hi-—Er—ys—ip—elo—tr—ich—al—es—————Erysipelotrichaceae-Erysipelotrichaceae Incertae S 0.0 0.6 0.042 We developed an oral antibiotic treatment protocol and characterized the effects 80% ————————————————————————Unknown-Unknown —————————————————————Ruminococcaceae-Unknown 2.2 0.0 0.007 0.3 0.037 ——————————————————Ruminococcaceae-Ruminococcaceae Incertae Sedis 0.4 0.0 0.025 0.0 0.044 —————————————————————Ruminococcaceae-Faecalibacterium of treatment on intestinal immune homeostasis and the burden and composition A B C D E 70% Mouse Weights 16s rDNA Copies Villus Length RELMβ in Stool —————————————————————Ruminococcaceae-Anaerotruncus 0.2 0.0 0.025 0.0 0.044 120 —————————————————Clostridia-Clostri—dia—le—s-———————————————Lachnospiraceae-Unknown 10.6 0.0 0.007 0.0 0.015 11 Firmicutes- of bacterial communities. Antibiotic administration resulted in cecal enlargement, 110 H2O 1.0×10 H2O *** ——————————————————Lachnospiraceae-Lachnospiraceae Incertae Sedis 1.0 0.0 0.007 0.0 0.015 110 60% ABX ABX H2O *** ——————————————————Lachnospiraceae-Coprococcus ** ——————————————————Lachnospiraceae-Butyrivibrio m 100 1.4 0.0 0.025 0.0 0.044 ——————————————————Lachnospiraceae-Bryantella lamina propria expansion, enterocyte hyperplasia, reduced RELMβ production, m 60 ** 10 50% 1.0×10 90 ——————————————————Lachnospiraceae-Acetitomaculum 105 ——————————————————Leuconostocaceae-Weissella 0.1 0.0 0.044 e 80 50 ————————————————————Bacilli-Lactobacillales- ——————————————————Lactobacillaceae-Lactobacillus and reduced production of the cytokines TNFα, IFNγ, IL-17A, IL-22, and IL-10 in g 70 40% Deferribacte—re—s ————————Deferribacteres-Deferr—ib—ac—ter—al—es—————————————Deferribacteraceae-Mucispirillum Copies/g n 09 40 ——————————————————U—nk—no—w—n-—Un—kn—ow—n———————————————————Unknown-Unknown 13.8 1.0 0.008 2.1 0.016 a 1.0×10 ABX H2O ABX GF ———————————————————————————Unknown-Unknown 41.9 1.8 0.008 4.3 0.016 the intestine, all consistent with reduced bacterial stimulation. Associated with h 100 0 1 5 9 30 30% ——————————————————Rikenellaceae-Unknown 1.9 0.1 0.010 C Day Villus Width ——————————————————Rikenellaceae-Marinilabilia 2.9 0.0 0.007 0.1 0.018 80 Pixel intensity 10 *** ——————————————————Rikenellaceae-Alistipes 7.3 1.9 0.016 these dramatic physiologic and anatomic changes, there was a ten-fold % 20 70 Bacteroidetes- ——————————————————Prevotellaceae-Xylanibacter 0.8 0.1 0.018 3.0 0.016 *** 20% ——————————Bacteroidetes-Bacteroidales- 60 ——————————————————Prevotellaceae-Unknown 1.2 0.1 0.031 5.2 0.016 m 10 ——————————————————Prevotellaceae-Prevotella 1.1 0.1 0.010 3.7 0.016 95 50 reduction in the amount of intestinal bacteria present. Sequencing of 16S rDNA GF m 1 ——————————————————Porphyromonadaceae-Unknown 0.9 0.0 0.010 0.0 0.015 Day 0 Day 1 Day 5 Day 9 10% 40 ——————————————————Porphyromonadaceae-Parabacteroides 0.4 47.0 0.008 21.3 0.016 sequences revealed a sharp reduction in the proportion of bacteria belonging to 30 ——————————————————Bacteroidaceae-Bacteroides 3.3 44.1 0.008 40.8 0.016 U—nk—no—w—n ——————————————Unknown-Un—kn—ow—n———————————————————Unknown-Unknown 0.7 0.0 0.010 0.1 0.034 20 0% 90 Fold change 0.1 H2O ABX GF 0 2 4 6 8 the Firmicutes phyla, while bacteria belonging to the Bacteroidetes and 1 3 5 7 9 0 1 5 9 Day Day Day Figure 4. A) Genus level phylogenetic classication of 16S rDNA frequencies in stool pellets collected from control-treated (H2O) or antibiotic-treated (ABX) Proteobacteria phyla persisted over time. In addition, we found significant animals from day 0 to day 9. B) Average frequency of bacterial groups before (Antibiotic Day 0) or during (Antibiotic Day 1, 9) antibiotic treatment. Mann- Figure 1. A) Weights of animals gavaged with unsupplemented (H2O; N=4) or antibiotic- Whitney P-values of changes in group frequency with antibiotic treatment. Frequency reductions upon antibiotic treatment in red, increases in green, non- temporal and spatial effects of antibiotics on luminal and mucosal-associated supplemented (ABX; N=5) water (± s.e.m). B) 16S rDNA gene copies as quantified from stool signicant changes blank. communities along the length of the colon including a reduction in the frequency pellets collected before (day 0) or over the course of antibiotic treatment (days 1, 5, 9) (N=5; ± Figure 5. Antibiotics modify luminal bacterial communities of mucosal-associated Lactobacillus. This comprehensive temporal and spatial s.e.m). C) Cecal images from control-treated (H2O), day 10 antibiotic-treated (ABX), or germ-free Cecum Prox. Colon Dist. Colon animals (GF) (bar 1 cm). D) Quantification of lamina propria expansion and enterocyte hyperpla- along the length of the colon. c c c d i i i t t t metagenomic analyses will provide a resource and framework to test the n e e e o o o u u u i i i e A B l l l b b b a a a g sia in the ceca from day 10 antibiotic-treated (ABX, N=5), as compared to control-treated (H2O; i i i O O O t t t v v v e 2 2 2 n - n - n - L influence of microbial communities in murine models of human metabolic and H2O ABX Phy—lum————————————Cl—as—s-—Or—de—r———————Family-Genus H A P H A P H A P N=4) or germ-free animals (GF; N=3) (***, p<0.001; ± s.e.m). E) Quantification of RELMβ protein 100% Verrucomicrob—ia ——————Verrucomicrobiae-V—er—ruc—o—mi—cro—b—ial—es————————————Verrucomicrobiaceae-Akkermansia 0.0 1.2 0.021 0.0 1.6 0.044 —T—M—7 ——————TM7 genera incertae sedis-Un—kn—ow—n———————————————————Unknown-Unknown inflammatory diseases. in stool pellets by western blot over the course of antibiotic treatment (N=5;**, P≤0.01; ± s.e.m). ————————Gammaproteobacteria-E—nte—ro—ba—c—ter—ial—es—————————————Enterobacteriaceae-Enterobacter 0.0 0.7 0.015 90% Proteobact—eri—a-———————Betaproteobacteria-Burkholderial—es———————————————————Unknown-Unknown 0.4 4.2 0.019 0.8 5.0 0.016 ———————————Alphaproteobacteria-Unknow—n———————————————————Unknown-Unknown —————————E—ry—sip—e—lot—ric—hi-—Er—ys—ip—elo—tr—ich—al—es—————Erysipelotrichaceae-Erysipelotrichaceae Incertae S 80% ————————————————————————Unknown-Unknown 1.2 0.3 0.029 Figure 2. Reduced cytokine production in the intestine —————————————————————Ruminococcaceae-Unknown 4.6 0.0 0.015 3.4 0.1 0.027 2.5 0.1 0.018 Introduction ——————————————————Ruminococcaceae-Ruminococcaceae Incertae Sedis 0.8 0.0 0.021 0.9 0.0 0.011 70% —————————————————————Ruminococcaceae-Faecalibacterium 0.9 0.0 0.042 of antibiotic-treated animals. —————————————————————Ruminococcaceae-Anaerotruncus 0.3 0.0 0.042 —————————————————Clostridia-Clostri—dia—le—s-———————————————Lachnospiraceae-Unknown 31.7 0.0 0.011 26.3 0.0 0.021 29.7 0.0 0.011 Firmicutes- ——————————————————Lachnospiraceae-Lachnospiraceae Incertae Sedis 1.7 0.0 0.011 1.8 0.0 0.021 1.9 0.0 0.011 60% • The human intestine is colonized by 100 trillion microorganisms ——————————————————Lachnospiraceae-Coprococcus 0.5 0.0 0.042 0.8 0.0 0.021 1.2 0.0 0.042 A tnfa ifng il17a il22 il10 ——————————————————Lachnospiraceae-Butyrivibrio 2.8 0.0 0.011 2.7 0.0 0.021 2.0 0.0 0.011 2 2 2 2 2 ——————————————————Lachnospiraceae-Bryantella 50% ——————————————————Lachnospiraceae-Acetitomaculum of which bacteria are the most abundant. ——————————————————Leuconostocaceae-Weissella ————————————————————Bacilli-Lactobacillales- ——————————————————Lactobacillaceae-Lactobacillus 40% Deferribacte—re—s————————Deferribacteres-Deferr—ib—ac—ter—al—es—————————————Deferribacteraceae-Mucispirillum 1.9 0.0 0.011 ——————————————————U—nk—no—w—n-—Un—kn—ow—n———————————————————Unknown-Unknown 8.4 1.6 0.016 10.6 1.6 0.029 10.4 2.1 0.016 • Intestinal bacteria promote proper digestion, metabolism, 1 1 1 1 1 ———————————————————————————Unknown-Unknown 26.0 2.7 0.016 31.5 3.8 0.029 28.8 3.8 0.016 30% ——————————————————Rikenellaceae-Unknown 1.3 0.3 0.029 *** * ——————————————————Rikenellaceae-Marinilabilia 1.4 0.2 0.018 ——————————————————Rikenellaceae-Alistipes 3.9 2.5 0.029 Relative Exp. *** epithelial cell function, angiogenesis, enteric nerve function, and Bacteroidetes- ——————————————————Prevotellaceae-Xylanibacter 1.3 2.5 0.029 *** ** 20% ——————————Bacteroidetes-Bacteroidales- 0 0 0 0 0 ——————————————————Prevotellaceae-Unknown ——————————————————Prevotellaceae-Prevotella 1.8 5.3 0.016 1.5 4.4 0.029 H2O ABX H2O ABX H2O ABX H2O ABX H2O ABX ——————————————————Porphyromonadaceae-Unknown 1.0 0.1 0.029 0.6 0.0 0.042 immune system development.
Load more

Recommended publications
  • 26Sor Em2rray /Mmucd
    D4006- Gut Microbiota Analysis UC Davis MMPC - Microbiome & Host Response Core Contents 1 Methods: 1 1.1 Sequencing . .1 1.2 Data processing . .1 2 Summary of Findings: 2 2.1 Sequencing analysis . .2 2.2 Microbial diversity . .2 2.2.1 Alpha Diversity . .2 2.2.2 Beta Diversity . 10 2.3 Data analysis using taxa abundance data . 13 2.3.1 Stacked bar graphs of Taxa abundances at each level . 14 A Appendix 1 (Taxa Abundance Tables) 30 B Appendix 2 (Taxa removed from filtered datasets at each level) 37 References: 43 Core Contacts: Helen E. Raybould, Ph.D., Core Leader ([email protected]) Trina A. Knotts, Ph.D., Core Co-Leader ([email protected]) Michael L. Goodson, Ph.D., Core Scientist ([email protected]) Client(s): Kent Lloyd, DVM PhD ;MMRRC; UC Davis Project #: MBP-2079 MMRRC strain ID: MMRRC_043514 Animal Information: The strain was donated to the MMRRC by Russell Ray at Baylor College of Medicine. Fecal samples were obtained from animals housed under the care of Russell Ray at Baylor College of Medicine. 1 Methods: Brief Project Description: MMRRC strains are often contributed to the MMRRC to fulfill the resource sharing aspects of NIH grants. Since transporting mice to another facilty often causes a microbiota shift, having a record of the original fecal microbiota from the donor institution where the original phenotyping or testing was performed may prove helpful if a phenotype is lost after transfer. Several MMRRC mouse lines were selected for fecal microbiota profiling of the microbiota. Table 1: Animal-Strain Information X.SampleID TreatmentGroup Animal_ID Genotype Line Sex MMRRC.043514.Mx054 MMRRC.043514_Het_M Mx054 Het MMRRC.043514 M MMRRC.043514.Mx415 MMRRC.043514_Het_M Mx415 Het MMRRC.043514 M 1 1.1 Sequencing Frozen fecal or regional gut samples were shipped on dry ice to UC Davis MMPC and Host Microbe Systems Biology Core.
    [Show full text]
  • Fe(II) Fe(III)
    Southern Illinois University Carbondale OpenSIUC Publications Department of Microbiology 2006 Microbes Pumping Iron: Anaerobic Microbial Iron Oxidation and Reduction Karrie A. Weber University of California - Berkeley Laurie A. Achenbach Southern Illinois University Carbondale, [email protected] John D. Coates University of California - Berkeley Follow this and additional works at: https://opensiuc.lib.siu.edu/micro_pubs Published in Nature Reviews Microbiology 4, 752-764 (October 2006), http://dx.doi.org/10.1038/ nrmicro1490. This Article is brought to you for free and open access by the Department of Microbiology at OpenSIUC. It has been accepted for inclusion in Publications by an authorized administrator of OpenSIUC. For more information, please contact [email protected]. 1 Microbes Pumping Iron: 2 Anaerobic Microbial Iron Oxidation and Reduction 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 Karrie A. Weber1, Laurie A. Achenbach2, and John D. Coates1* 18 19 20 21 22 23 1Department of Plant and Microbial Biology 24 271 Koshland Hall 25 University of California, Berkeley 26 Berkeley, CA 94720 27 28 29 2Department of Microbiology 30 Southern Illinois University 31 Carbondale, IL 62901 32 33 34 35 Corresponding Author 36 Tel: (510) 643-8455 37 Fax: (510) 642-4995 38 e-mail: [email protected] 39 1 1 Abstract 2 Iron (Fe) has long been a recognized physiological requirement for life, yet its role for a 3 broad diversity of microorganisms persisting in water, soils, and sediments extends well-beyond 4 a nutritional necessity. Microorganisms from within both the domain Archaea and Bacteria are 5 capable of metabolically exploiting the favorable redox potential between the Fe(III)/Fe(II) 6 couple.
    [Show full text]
  • Supplementary Material Impacts of Radiation on the Bacterial And
    Supplementary Material Impacts of radiation on the bacterial and fungal microbiome of small mammals in the Chernobyl Exclusion Zone Rachael E. Antwis, Nicholas A. Beresford, Joseph A. Jackson, Ross Fawkes, Catherine L. Barnett, Elaine Potter, Lee Walker, Sergey Gaschak, Michael D. Wood Table S1 Sample sizes of host species used in the study, and associated sex, total absorbed dose rate, burn and site categories for these samples. Animals estimated to receive total absorbed dose rates of <4 µGy h-1 were assigned ‘low’, those with estimated dose rates of 4-42 µGy h-1 assigned ‘medium’, and those >42 µGy h-1 assigned to the ‘high’ category. All samples from 2017 were collected within the Red Forest but from areas that had experienced different degrees of damage from forest fires. Samples from 2018 were either collected within or outside the Red Forest. Sampling information Sex Total absorbed dose category Burn category Site category Year Sample Host species Total n Female Male Unidentified Low Medium High Burnt Burnt Unburnt Inside Red Outside type (regrowth) (minimal Forest Red regrowth) Forest 2017 Faeces Bank vole 22 5 16 1 0 0 22 3 1 18 All - 2017 Faeces Striped field mouse 29 10 18 1 0 7 22 15 0 14 All - 2017 Faeces Wood mouse 27 6 20 1 0 0 27 2 25 0 All - 2017 Faeces Yellow-necked mouse 58 28 29 1 0 7 51 19 17 22 All - 2018 Gut Bank vole 142 59 83 0 42 64 36 - - - 34 108 (caecum) RESULTS Differences in community composition between host species and sample types Wood mice and yellow-necked mice had a similar bacterial community composition to one another (Figure 1a), with the exception of the family Helicobacteraceae (Z = 2.982, p = 0.023; Figure 1c).
    [Show full text]
  • Supplementary Table S1. Fisher Pairwise Comparisons of Lagoon and House Pathogen Levels (CFU/Gvss Log10) Season System Site Fecal Coliforms E
    Supplementary Table S1. Fisher pairwise comparisons of lagoon and house pathogen levels (CFU/gVSS log10) Season System Site Fecal coliforms E. coli Enterococcus sp. Spring Open Lagoon 6.00 g1 5.46 hi 5.91 cd House 6.57 e 6.33 cd 6.35 b Cover Lagoon 6.00 g 5.60 gh 5.44 f House 7.73 a 7.63 a 5.87 cd Summer Open Lagoon 6.35 f 5.83 f 5.94 cd House 7.83 a 6.10 e 6.73 a Cover Lagoon 7.04 c 6.47 c 5.86 cd House 7.42 b 6.71 b 6.07 c Fall Open Lagoon 5.58 i 5.58 gh 5.56 ef House 6.81 d 6.72 b 6.01 c Cover Lagoon 5.99 g 5.34 i 5.50 f House 6.38 f 6.19 de 5.74 de Winter Open Lagoon 5.41 j 5.13 j 4.88 g House 6.06 g 5.61 gh 6.67 a Cover Lagoon 5.73 h 5.73 fg 5.44 f House 6.34 f 6.25 de 5.86 cd 1Means followed by the same letter are not significantly different at p = 0.05 Supplementary Table S2. Relative abundances of OTUs identified using universal bacterial primer set, presented as relative abundances (%) Only bacterial families are counted in Figure 5 and discussion involving bacterial family identification. # Identified in # Identified from all 8 All 16 All #OTU Table SpOLRA SuOLRA FOLRA WOLRA SpCLRA SuCLRA FCLRA WCLRA SpOHRA SuOHRA FOHRA WOHRA SpCHRA SuCHRA FCHRA WCHRA all samples lagoon samples Samples Lagoons Notes Key Patulibacteraceae 0 9.93739E‐05* 0.000134 0.000116 0 0 0 0 0 0 0.000452 0 0 0 0 0 4 3 Sp = Spring O = Open Ruaniaceae 0 0 0 0 0 0 0 0 0 0 0 0 0 0.000221577 0 7.73E‐05 2 0 Su = Summer C = Covered Thermoactinomycetaceae 0 0 0.000267 0.000116 0 0.00037092 0.000529 0.000526 0 0.000342922 0.000271 0.000197 0 0 0 0 8 5 F = Fall L = Lagoon Beutenbergiaceae 0.000226334 0.000331246 0.000579 0.001663 0.000620176 0 0.000106 0.000807 0.002320743 0.000571537 0.000723 0.000591 0.000169731 0 0.000606 0 13 7 W = Winter H = House Thermoanaerobacterales Family III.
    [Show full text]
  • Molecular Analyses of Changes Induced in the Microbial Populations of Murine Colon After As(III) Exposure Rishu Dheer
    Duquesne University Duquesne Scholarship Collection Electronic Theses and Dissertations Summer 2011 Molecular Analyses of Changes Induced in the Microbial Populations of Murine Colon After As(III) Exposure Rishu Dheer Follow this and additional works at: https://dsc.duq.edu/etd Recommended Citation Dheer, R. (2011). Molecular Analyses of Changes Induced in the Microbial Populations of Murine Colon After As(III) Exposure (Doctoral dissertation, Duquesne University). Retrieved from https://dsc.duq.edu/etd/484 This Immediate Access is brought to you for free and open access by Duquesne Scholarship Collection. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of Duquesne Scholarship Collection. For more information, please contact [email protected]. MOLECULAR ANALYSES OF CHANGES INDUCED IN THE MICROBIAL POPULATIONS OF MURINE COLON AFTER As (III) EXPOSURE A Dissertation Submitted to Bayer School of Natural and Environmental Sciences Duquesne University In partial fulfillment of the requirements for the degree of Doctor of Philosophy By Rishu Dheer August, 2011 Copyright by Rishu Dheer 2011 MOLECULAR ANALYSES OF CHANGES INDUCED IN THE MICROBIAL POPULATIONS OF MURINE COLON AFTER As (III) EXPOSURE By Rishu Dheer Approved June 14, 2011 ________________________________ ________________________________ Dr. John F. Stolz Dr. Aaron Barchowsky Director, Center of Environmental Associate Professor of Biology Research and Education (Committee Member) Professor of Biology (Committee Chair) ________________________________
    [Show full text]
  • Oral Sub-Chronic Ochratoxin a Exposure Induces Gut Microbiota Alterations in Mice
    toxins Article Oral Sub-Chronic Ochratoxin a Exposure Induces Gut Microbiota Alterations in Mice María Izco 1 , Ariane Vettorazzi 2,3 , Maria de Toro 4, Yolanda Sáenz 5 and Lydia Alvarez-Erviti 1,* 1 Laboratory of Molecular Neurobiology, Center for Biomedical Research of La Rioja (CIBIR), 26006 Logroño, Spain; [email protected] 2 MITOX Group, Department of Pharmacology and Toxicology, Faculty of Pharmacy, Universidad de Navarra, 31008 Pamplona, Spain; [email protected] 3 IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain 4 Center for Biomedical Research of La Rioja (CIBIR), Genomics and Bioinformatics Core Facility, 26006 Logroño, Spain; [email protected] 5 Molecular Microbiology Area, Center for Biomedical Research of La Rioja (CIBIR), 26006 Logroño, Spain; [email protected] * Correspondence: [email protected]; Tel.: +34-941-278-875 Abstract: Gut microbiota plays crucial roles in maintaining host health. External factors, such as diet, medicines, and environmental toxins, influence the composition of gut microbiota. Ochratoxin A (OTA) is one of the most prevalent and relevant mycotoxins and is a highly abundant food and animal feed contaminant. In the present study, we aimed to investigate OTA gut microbiome toxicity in mice sub-chronically exposed to low doses of OTA (0.21, 0.5, and 1.5 mg/kg body weight) by daily oral gavage for 28 days. Fecal microbiota from control and OTA-treated mice was analyzed using 16S ribosomal RNA (rRNA) gene sequencing followed by metagenomics. OTA exposure caused marked changes in gut microbial community structure, including the decrease in the diversity of fecal microbiota and the relative abundance of Firmicutes, as well as the increase in the relative abundance of Bacteroidetes at the phylum level.
    [Show full text]
  • Pan-Genome Analyses of 24 Shewanella Strains Re-Emphasize
    Zhong et al. Biotechnol Biofuels (2018) 11:193 https://doi.org/10.1186/s13068-018-1201-1 Biotechnology for Biofuels RESEARCH Open Access Pan‑genome analyses of 24 Shewanella strains re‑emphasize the diversifcation of their functions yet evolutionary dynamics of metal‑reducing pathway Chaofang Zhong, Maozhen Han, Shaojun Yu, Pengshuo Yang, Hongjun Li and Kang Ning* Abstract Background: Shewanella strains are important dissimilatory metal-reducing bacteria which are widely distributed in diverse habitats. Despite eforts to genomically characterize Shewanella, knowledge of the molecular components, functional information and evolutionary patterns remain lacking, especially for their compatibility in the metal- reducing pathway. The increasing number of genome sequences of Shewanella strains ofers a basis for pan-genome studies. Results: A comparative pan-genome analysis was conducted to study genomic diversity and evolutionary relation- ships among 24 Shewanella strains. Results revealed an open pan-genome of 13,406 non-redundant genes and a core-genome of 1878 non-redundant genes. Selective pressure acted on the invariant members of core genome, in which purifying selection drove evolution in the housekeeping mechanisms. Shewanella strains exhibited extensive genome variability, with high levels of gene gain and loss during the evolution, which afected variable gene sets and facilitated the rapid evolution. Additionally, genes related to metal reduction were diversely distributed in Shewanella strains and evolved under purifying selection, which highlighted the basic conserved functionality and specifcity of respiratory systems. Conclusions: The diversity of genes present in the accessory and specifc genomes of Shewanella strains indicates that each strain uses diferent strategies to adapt to diverse environments.
    [Show full text]
  • Gut Microbiota Analysis UC Davis MMPC - Microbiome & Host Response Core
    D4006- Gut Microbiota Analysis UC Davis MMPC - Microbiome & Host Response Core Contents 1 Methods: 1 1.1 Sequencing . .1 1.2 Data processing . .1 2 Summary of Findings: 2 2.1 Sequencing analysis . .2 2.2 Microbial diversity . .2 2.2.1 Alpha Diversity . .2 2.2.2 Beta Diversity . 10 2.3 Data analysis using taxa abundance data . 13 2.3.1 Stacked bar graphs of Taxa abundances at each level . 14 A Appendix 1 (Taxa Abundance Tables) 30 B Appendix 2 (Taxa removed from filtered datasets at each level) 37 References: 43 Core Contacts: Helen E. Raybould, Ph.D., Core Leader ([email protected]) Trina A. Knotts, Ph.D., Core Co-Leader ([email protected]) Michael L. Goodson, Ph.D., Core Scientist ([email protected]) Client(s): Kent Lloyd, DVM PhD ;MMRRC; UC Davis Project #: MBP-2079 MMRRC strain ID: MMRRC_043568 Animal Information: The strain was donated to the MMRRC by Michael Mitchell at Inserm. Fecal samples were obtained from animals housed under the care of Arthur Arnold at UCLA. 1 Methods: Brief Project Description: MMRRC strains are often contributed to the MMRRC to fulfill the resource sharing aspects of NIH grants. Since transporting mice to another facilty often causes a microbiota shift, having a record of the original fecal microbiota from the donor institution where the original phenotyping or testing was performed may prove helpful if a phenotype is lost after transfer. Several MMRRC mouse lines were selected for fecal microbiota profiling of the microbiota. Table 1: Animal-Strain Information X.SampleID TreatmentGroup Animal_ID Genotype Line Sex MMRRC.043568.M93054 MMRRC.043568_Tg.plus_M M93054 Tg.plus MMRRC.043568 M MMRRC.043568.M06285 MMRRC.043568_Tg.plus_M M06285 Tg.plus MMRRC.043568 M 1 1.1 Sequencing Frozen fecal or regional gut samples were shipped on dry ice to UC Davis MMPC and Host Microbe Systems Biology Core.
    [Show full text]
  • Comprehensive Comparative Genomics Reveals Over 50 Phyla of Free‑Living and Pathogenic Bacteria Are Associated with Diverse Members of the Amoebozoa Yonas I
    www.nature.com/scientificreports OPEN Comprehensive comparative genomics reveals over 50 phyla of free‑living and pathogenic bacteria are associated with diverse members of the amoebozoa Yonas I. Tekle*, Janae M. Lyttle, Maya G. Blasingame & Fang Wang The Amoebozoa, a group containing predominantly amoeboid unicellular protists has been shown to play an important ecological role in controlling environmental bacteria. Amoebozoans not only graze bacteria but also serve as a safe niche for bacterial replication and harbor endosymbiotic bacteria including dangerous human pathogens. Despite their importance, only a few lineages of Amoebozoa have been studied in this regard. In this research, we conducted a comprehensive genomic and transcriptomic study with expansive taxon sampling by including representatives from the three known clades of the Amoebozoa. We used culture independent whole culture and single cell genomics/transcriptomics to investigate the association of bacteria with diverse amoebozoans. Relative to current published evidence, we recovered the largest number of bacterial phyla (64) and human pathogen genera (51) associated with the Amoebozoa. Using single cell genomics/ transcriptomics we were able to determine up to 24 potential endosymbiotic bacterial phyla, some potentially endosymbionts. This includes the majority of multi‑drug resistant pathogens designated as major public health threats. Our study demonstrates amoebozoans are associated with many more phylogenetically diverse bacterial phyla than previously recognized. It also shows that all amoebozoans are capable of harboring far more dangerous human pathogens than presently documented, making them of primal public health concern. Te study of microbial interactions is a complex and fascinating feld of research 1–3. Microorganisms occupy diverse ecological niches and are usually found in large communities that result in inherent interactions.
    [Show full text]
  • Phylogeny Reveals Novel Hipa-Homologous Kinase Families
    bioRxiv preprint doi: https://doi.org/10.1101/2021.04.14.439929; this version posted April 16, 2021. 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. Phylogeny Reveals Novel HipA-Homologous Kinase Families and Toxin – Antitoxin Gene Organizations Kenn Gerdes1*, Rene Bærentsen2 & Ditlev E. Brodersen2* 1) Centre of Excellence for Bacterial Stress Response and Persistence, Section for Functional Genomics, Department of Biology, University of Copenhagen, DK-2200, Copenhagen N, Denmark. 2) Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark. * To whom correspondence should be addressed: [email protected] or [email protected] Running Head: Phylogeny of High Persister A-Homologous Kinases Keywords: High Persister A, HipB, HipS, HipT, HIRAN, Stl, GltX, TrpS bioRxiv preprint doi: https://doi.org/10.1101/2021.04.14.439929; this version posted April 16, 2021. 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. Abstract Toxin – Antitoxin modules function in the genetic stability of mobile genetic elements, bacteriophage defense, and antibiotic tolerance. A gain-of-function mutation of the Escherichia coli K-12 hipBA module can induce antibiotic tolerance in a subpopulation of bacterial cells, a phenomenon known as persistence. HipA is a Ser/Thr kinase that phosphorylates and inactivates glutamyl tRNA synthetase, inhibiting cellular translation and inducing the stringent response.
    [Show full text]
  • Electron Donors and Acceptors for Members of the Family Beggiatoaceae
    Electron donors and acceptors for members of the family Beggiatoaceae Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften - Dr. rer. nat. - dem Fachbereich Biologie/Chemie der Universit¨at Bremen vorgelegt von Anne-Christin Kreutzmann aus Hildesheim Bremen, November 2013 Die vorliegende Doktorarbeit wurde in der Zeit von Februar 2009 bis November 2013 am Max-Planck-Institut f¨ur marine Mikrobiologie in Bremen angefertigt. 1. Gutachterin: Prof. Dr. Heide N. Schulz-Vogt 2. Gutachter: Prof. Dr. Ulrich Fischer 3. Pr¨uferin: Prof. Dr. Nicole Dubilier 4. Pr¨ufer: Dr. Timothy G. Ferdelman Tag des Promotionskolloquiums: 16.12.2013 To Finn Summary The family Beggiatoaceae comprises large, colorless sulfur bacteria, which are best known for their chemolithotrophic metabolism, in particular the oxidation of re- duced sulfur compounds with oxygen or nitrate. This thesis contributes to a more comprehensive understanding of the physiology and ecology of these organisms with several studies on different aspects of their dissimilatory metabolism. Even though the importance of inorganic sulfur substrates as electron donors for the Beggiatoaceae has long been recognized, it was not possible to derive a general model of sulfur compound oxidation in this family, owing to the fact that most of its members can currently not be cultured. Such a model has now been developed by integrating information from six Beggiatoaceae draft genomes with available literature data (Section 2). This model proposes common metabolic pathways of sulfur compound oxidation and evaluates whether the involved enzymes are likely to be of ancestral origin for the family. In Section 3 the sulfur metabolism of the Beggiatoaceae is explored from a dif- ferent perspective.
    [Show full text]
  • Metagenome-Assembled Genomes Provide New Insight Into The
    www.nature.com/scientificreports Corrected: Author Correction OPEN Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal Received: 17 August 2018 Accepted: 17 January 2019 pools in Kamchatka, Russia Published online: 28 February 2019 Laetitia G. E. Wilkins1,2, Cassandra L. Ettinger 2, Guillaume Jospin2 & Jonathan A. Eisen 2,3,4 Culture-independent methods have contributed substantially to our understanding of global microbial diversity. Recently developed algorithms to construct whole genomes from environmental samples have further refned, corrected and revolutionized understanding of the tree of life. Here, we assembled draft metagenome-assembled genomes (MAGs) from environmental DNA extracted from two hot springs within an active volcanic ecosystem on the Kamchatka peninsula, Russia. This hydrothermal system has been intensively studied previously with regard to geochemistry, chemoautotrophy, microbial isolation, and microbial diversity. We assembled genomes of bacteria and archaea using DNA that had previously been characterized via 16S rRNA gene clone libraries. We recovered 36 MAGs, 29 of medium to high quality, and inferred their placement in a phylogenetic tree consisting of 3,240 publicly available microbial genomes. We highlight MAGs that were taxonomically assigned to groups previously underrepresented in available genome data. This includes several archaea (Korarchaeota, Bathyarchaeota and Aciduliprofundum) and one potentially new species within the bacterial genus Sulfurihydrogenibium. Putative functions in both pools were compared and are discussed in the context of their diverging geochemistry. This study adds comprehensive information about phylogenetic diversity and functional potential within two hot springs in the caldera of Kamchatka. Terrestrial hydrothermal systems are of great interest to the general public and to scientists alike due to their unique and extreme conditions.
    [Show full text]