Papers by Andrew J Fabich
We previously isolated a spontaneous mutant of Escherichia coli K-12, strain MG1655, following pa... more We previously isolated a spontaneous mutant of Escherichia coli K-12, strain MG1655, following passage through the streptomycin-treated mouse intestine, that has colonization traits superior to the wild-type parent strain (M. P. Leatham et al., Infect. Immun. 73:8039–8049, 2005). This intestine-adapted strain (E. coli MG1655*) grew faster on several different carbon sources than the wild type and was nonmotile due to deletion of the flhD gene. We now report the results of several high-throughput genomic analysis approaches to further characterize E. coli MG1655*. Whole-genome pyrosequencing did not reveal any changes on its genome, aside from the deletion at the flhDC locus, that could explain the colonization advantage of E. coli MG1655*. Microarray analysis revealed modest yet significant induction of catabolic gene systems across the genome in both E. coli MG1655* and an isogenic flhD mutant constructed in the laboratory. Catabolome analysis with Biolog GN2 microplates revealed a...
Mammals are aerobes that harbor an intestinal ecosystem dominated by large numbers of anaerobic m... more Mammals are aerobes that harbor an intestinal ecosystem dominated by large numbers of anaerobic microorganisms. However, the role of oxygen in the intestinal ecosystem is largely unexplored. We used systematic mutational analysis to determine the role of respiratory metabolism in the streptomycin-treated mouse model of intestinal colonization. Here we provide evidence that aerobic respiration is required for commensal and pathogenic Escherichia coli to colonize mice. Our results showed that mutants lacking ATP synthase, which is required for all respiratory energy-conserving metabolism, were eliminated by competition with respiratory-competent wild-type strains. Mutants lacking the high-affinity cytochrome bd oxidase, which is used when oxygen tensions are low, also failed to colonize. However, the low-affinity cytochrome bo3 oxidase, which is used when oxygen tension is high, was found not to be necessary for colonization. Mutants lacking either nitrate reductase or fumarate reduct...
Enterohemorrhagic Escherechia coli is a serious human pathogen causing bloody diarrhea and hemoly... more Enterohemorrhagic Escherechia coli is a serious human pathogen causing bloody diarrhea and hemolytic uremic syndrome. It is difficult to study in animal models, but pathogenesis may be modeled in mice with the similar murine pathogen, Citrobacter rodentium. C. rodentium does not cause disease in streptomycin-treated mice, suggesting that it is competition with other facultative anaerobes that triggers pathogenesis. Streptomycin-treated mice were co-colonized with C. rodentium and a commensal E. coli strain. The intestinal microbiota of each group was observed over a 15-day period using quantitative PCR. Colon weights were also measured over the same period. Results indicate that the disease caused by competition is not similar to normal C. rodentium pathogenesis. Further research is necessary to determine the precise mechanism of pathogenesis in this experimental model. The outcome may provide new insight into enterohemorrhagic E. coli prevention and treatment. COLONIZATION OF INTES...
ISSN: 1937-9056 Copyright © 2018 Answers in Genesis, Inc. All content is owned by Answers in Gene... more ISSN: 1937-9056 Copyright © 2018 Answers in Genesis, Inc. All content is owned by Answers in Genesis (“AiG”) unless otherwise indicated. AiG consents to unlimited copying and distribution of print copies of Answers Research Journal articles for non-commercial, non-sale purposes only, provided the following conditions are met: the author of the article is clearly identified; Answers in Genesis is acknowledged as the copyright owner; Answers Research Journal and its website, www.answersresearchjournal.org, are acknowledged as the publication source; and the integrity of the work is not compromised in any way. For website and other electronic distribution and publication, AiG consents to republication of article abstracts with direct links to the full papers on the ARJ website. All rights reserved. For more information write to: Answers in Genesis, PO Box 510, Hebron, KY 41048, Attn: Editor, Answers Research Journal. The views expressed are those of the writer(s) and not necessarily th...
The Proceedings of the International Conference on Creationism, 2018
Devotional Biology is being developed as a one-semester college-level conceptual biology textbook... more Devotional Biology is being developed as a one-semester college-level conceptual biology textbook for non-science majors. Except for presenting a survey of organisms and an introduction to organismal anatomy and physiology (typically reserved for a second-semester course), Devotional Biology covers all the major topics of biology presented in secular texts as well as a few others not usually covered at all. Student surveys indicate students believe they learn biology through the Devotional Biology text. At the same time, Devotional Biology presents biology from the perspective of a distinctly biblical worldview-and on surveys, Devotional Biology students believe they improved their appreciation of biology as well. Devotional Biology also focuses on God, and how His attributes are evident in the biological world-and on surveys, Devotional Biology students believe they improved their recognition of God in the creation, their understanding of God, their relationship to God, and their use of the creation in witness to others. Devotional Biology also assumes a young-age creationist interpretation of biology, critiquing the naturalistic perspective of the field in the process-and on surveys, Devotional Biology students believe they grew in their faith and learned to defend their faith. Devotional Biology also includes responsibilities of believers as priests and kings in God's creation-and on surveys, Devotional Biology students believe they grew in their understanding of their ethical responsibilities, in their worship of God, and in better ruling over the creation. KEY WORDS college, textbook, conceptual biology, biblical worldview, young-age creationism, holism, macro-to-micro
Gastroenterology, 2017
Enteropathogenic Escherichia coli (EPEC) is a foodborne pathogen that uses a type III secretion s... more Enteropathogenic Escherichia coli (EPEC) is a foodborne pathogen that uses a type III secretion system to translocate effector molecules into host intestinal epithelial cells causing diarrhea. EPEC effectors subvert several host cell signaling cascades balancing pro-and anti-inflammatory pathways; thus EPEC does not induce a robust intestinal inflammatory response as other enteric pathogens. Homologous EPEC effector proteins, NleH1 and NleH2, have been shown to suppress apoptosis. While NleH1 also suppresses the NF-κB pathway, NleH2 can either activate or suppress this pathway depending on the in vitro conditions. We found that in mice administered DSS (known to activate ERK1/2, p38 and apoptosis), NleH1 is much more potent than H2 in suppressing P-ERK1/2 activation and improving colitis and survival. We hypothesized that NleH1 inhibits additional signaling cascades increasing its anti-inflammatory effects. The impact of NleH1 and H2 on p38 activation (Phospho-p38) and apoptosis (cleaved caspase-3) was assessed by inducing colitis in mice using DSS, then infecting with wild type (WT) EPEC, WT overexpressing NleH1, ∆nleH1/H2, ∆nleH1/H2 complemented to express NleH1 or H2 or NleH1-K159A (site-directed mutant unable to suppress NF-κB). Colonic tissues were assessed for P-p38 and cleaved caspase-3 by immunofluorescence microscopy. P-p38 increased 2-fold in mice with DSS colitis compared to controls (213%; n=4; p<0.001). Infection of DSS colitis mice with ∆nleH1/H2 significantly increased P-p38 above levels induced by DSS alone (36%; n=4; p<0.001). Complementation of ∆nleH1/H2 with either NleH1 or NleH2 decreased DSS-activated P-p38 by 25 and 20%, resp (n=4; p<0.01). Infection with WT or WT overexpressing NleH1 reduced P-p38 by 40% (n=4; p<0.001). Complementing ∆nleH1/H2 with NleH1-K159A nearly abolished P-p38 suppression, reducing levels by only 11% compared to DSS alone indicating K159 is essential for both p38 and NF-κB suppression. Cleaved caspase-3 was suppressed at least by all strains except ∆nleH1/H2 (n=4; p<0.01). Serum cytokine levels showed that infection of DSS-treated mice with ∆nleH1/H2 complemented with NleH1-K159A failed to suppress IL-12(p70) and IFNγ compared to those infected with WT-NleH1 (n=3, p<0.05) indicating the essential role of K159 in reducing inflammation in vivo. Based on these data, we conclude that NleH1 attenuates intestinal inflammation by suppressing several key signaling cascades including NF-κB, ERK1/2, and p38 and reducing apoptosis. Constitutive activation of NF-κB does not cause destructive inflammation unless accompanied by active MAPK; both of
Genome announcements, 2015
Citrobacter rodentium is a Gram-negative bacterium which causes transmissible murine colonic hype... more Citrobacter rodentium is a Gram-negative bacterium which causes transmissible murine colonic hyperplasia and models the virulence of enterohemorrhagic Escherichia coli in vivo. Thus, C. rodentium is used to study human gastrointestinal disease. We present the draft genome sequence of C. rodentium strain ATCC 51459, also known as DBS100.
Veterinary Microbiology, 2009
Infection and Immunity, 2011
We previously isolated a spontaneous mutant of Escherichia coli K-12, strain MG1655, following pa... more We previously isolated a spontaneous mutant of Escherichia coli K-12, strain MG1655, following passage through the streptomycin-treated mouse intestine, that has colonization traits superior to the wild-type parent strain (M. P. Leatham et al., Infect. Immun. 73:8039-8049, 2005). This intestine-adapted strain (E. coli MG1655*) grew faster on several different carbon sources than the wild type and was nonmotile due to deletion of the flhD gene. We now report the results of several high-throughput genomic analysis approaches to further characterize E. coli MG1655*. Whole-genome pyrosequencing did not reveal any changes on its genome, aside from the deletion at the flhDC locus, that could explain the colonization advantage of E. coli MG1655*.
Infection and Immunity, 2007
Mammals are aerobes that harbor an intestinal ecosystem dominated by large numbers of anaerobic m... more Mammals are aerobes that harbor an intestinal ecosystem dominated by large numbers of anaerobic microorganisms. However, the role of oxygen in the intestinal ecosystem is largely unexplored. We used systematic mutational analysis to determine the role of respiratory metabolism in the streptomycin-treated mouse model of intestinal colonization. Here we provide evidence that aerobic respiration is required for commensal and pathogenic Escherichia coli to colonize mice. Our results showed that mutants lacking ATP synthase, which is required for all respiratory energy-conserving metabolism, were eliminated by competition with respiratory-competent wild-type strains. Mutants lacking the high-affinity cytochrome bd oxidase, which is used when oxygen tensions are low, also failed to colonize. However, the low-affinity cytochrome bo 3 oxidase, which is used when oxygen tension is high, was found not to be necessary for colonization. Mutants lacking either nitrate reductase or fumarate reductase also had major colonization defects. The results showed that the entire E. coli population was dependent on both microaerobic and anaerobic respiration, consistent with the hypothesis that the E. coli niche is alternately microaerobic and anaerobic, rather than static. The results indicate that success of the facultative anaerobes in the intestine depends on their respiratory flexibility. Despite competition for relatively scarce carbon sources, the energy efficiency provided by respiration may contribute to the widespread distribution (i.e., success) of E. coli strains as commensal inhabitants of the mammalian intestine.
Infection and Immunity, 2008
The carbon sources that support the growth of pathogenic Escherichia coli O157:H7 in the mammalia... more The carbon sources that support the growth of pathogenic Escherichia coli O157:H7 in the mammalian intestine have not previously been investigated. In vivo, the pathogenic E. coli EDL933 grows primarily as single cells dispersed within the mucus layer that overlies the mouse cecal epithelium. We therefore compared the pathogenic strain and the commensal E. coli strain MG1655 modes of metabolism in vitro, using a mixture of the sugars known to be present in cecal mucus, and found that the two strains used the 13 sugars in a similar order and cometabolized as many as 9 sugars at a time. We conducted systematic mutation analyses of E. coli EDL933 and E. coli MG1655 by using lesions in the pathways used for catabolism of 13 mucus-derived sugars and five other compounds for which the corresponding bacterial gene system was induced in the transcriptome of cells grown on cecal mucus. Each of 18 catabolic mutants in both bacterial genetic backgrounds was fed to streptomycin-treated mice, together with the respective wild-type parent strain, and their colonization was monitored by fecal plate counts. None of the mutations corresponding to the five compounds not found in mucosal polysaccharides resulted in colonization defects. Based on the mutations that caused colonization defects, we determined that both E. coli EDL933 and E. coli MG1655 used arabinose, fucose, and N-acetylglucosamine in the intestine. In addition, E. coli EDL933 used galactose, hexuronates, mannose, and ribose, whereas E. coli MG1655 used gluconate and N-acetylneuraminic acid. The colonization defects of six catabolic lesions were found to be additive with E. coli EDL933 but not with E. coli MG1655. The data indicate that pathogenic E. coli EDL933 uses sugars that are not used by commensal E. coli MG1655 to colonize the mouse intestine. The results suggest a strategy whereby invading pathogens gain advantage by simultaneously consuming several sugars that may be available because they are not consumed by the commensal intestinal microbiota.
American Journal of Veterinary Research, 2006
Objective-To develop a repeatable model for studying colonization with streptomycin-resistant Esc... more Objective-To develop a repeatable model for studying colonization with streptomycin-resistant Escherichia coli O157:H7 in adult cattle. Animals-5 adult mixed-breed beef cattle. Procedures-Cattle were surgically cannulated in the duodenum, treated daily with streptomycin (33 mg/kg) via the duodenal cannula prior to and during experimental colonizations, and colonized with 10 10 CFUs of streptomycin-resistant E coli O157:H7 via the duodenal cannula. Colonization of rectal mucus and shedding in feces were monitored. Antimicrobials were administered to eliminate the colonizing strain so that 5 repeated colonization experiments could be performed. A comprehensive analysis of colonization was performed at necropsy. Results-Streptomycin treatment resulted in improved experimental colonization variables, compared with untreated controls, during initiation (days 2 to 6) and early maintenance (days 7 to 12) of colonization. Elimination of the colonizing strain followed by 5 repeated colonizations in the same animals indicated the repeatability of the protocol. Positive results of bacteriologic culture of feces 7 and 12 days after colonization were obtained in 100% and 84% of samples, respectively, across all animals and trials. At necropsy, highest magnitude recovery was in terminal rectal mucus. Conclusions and Clinical Relevance-The model was highly repeatable and novel with respect to streptomycin treatment, use of duodenal cannulas, and repeated colonizations of the same animals. Its use in adult cattle, from which most bovine-derived food originates, is critical to the study of preharvest food safety. The findings have implications for understanding intermittency of shedding in the field and for proposed vaccine-based interventions. (Am J Vet Res
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Papers by Andrew J Fabich