Escherichia coli Strains Producing Selected Bacteriocins Inhibit Porcine Enterotoxigenic Escherichia coli (ETEC) under both In Vitro and In Vivo Conditions
Jazyk angličtina Země Spojené státy americké Médium print-electronic
Typ dokumentu časopisecké články, randomizované kontrolované studie veterinární, práce podpořená grantem
PubMed
33962981
PubMed Central
PMC8231719
DOI
10.1128/aem.03121-20
PII: AEM.03121-20
Knihovny.cz E-zdroje
- Klíčová slova
- E. coli, ETEC, Escherichia, STEC, bacteriocin, pig, probiotic,
- MeSH
- bakteriální toxiny * metabolismus MeSH
- bakteriociny metabolismus terapeutické užití MeSH
- Escherichia coli * účinky léků genetika metabolismus MeSH
- faktory virulence genetika MeSH
- feces mikrobiologie MeSH
- infekce vyvolané Escherichia coli mikrobiologie prevence a kontrola veterinární MeSH
- nemoci prasat mikrobiologie prevence a kontrola MeSH
- prasata MeSH
- probiotika terapeutické užití MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- randomizované kontrolované studie veterinární MeSH
- Názvy látek
- bakteriální toxiny * MeSH
- bakteriociny MeSH
- faktory virulence MeSH
Enterotoxigenic Escherichia coli (ETEC) and Shiga toxin-producing E. coli (STEC) strains are the causative agents of severe foodborne diseases in both humans and animals. In this study, porcine pathogenic E. coli strains (n = 277) as well as porcine commensal strains (n = 188) were tested for their susceptibilities to 34 bacteriocin monoproducers to identify the most suitable bacteriocin types inhibiting porcine pathogens. Under in vitro conditions, the set of pathogenic E. coli strains was found to be significantly more susceptible to the majority of tested bacteriocins than commensal E. coli. Based on the production of bacteriocins with specific activity against pathogens, three potentially probiotic commensal E. coli strains of human origin were selected. These strains were found to be able to outcompete ETEC strains expressing F4 or F18 fimbriae in liquid culture and also decreased the severity and duration of diarrhea in piglets during experimental ETEC infection as well as pathogen numbers on the last day of in vivo experimentation. While the extents of the probiotic effect were different for each strain, the cocktail of all three strains showed the most pronounced beneficial effects, suggesting synergy between the tested E. coli strains. IMPORTANCE Increasing levels of antibiotic resistance among bacteria also increase the need for alternatives to conventional antibiotic treatment. Pathogenic Escherichia coli represents a major diarrheic infectious agent of piglets in their postweaning period; however, available measures to control these infections are limited. This study describes three novel E. coli strains producing antimicrobial compounds (bacteriocins) that actively inhibit a majority of toxigenic E. coli strains. The beneficial effect of three potentially probiotic E. coli strains was demonstrated under both in vitro and in vivo conditions. The novel probiotic candidates may be used as prophylaxis during piglets' postweaning period to overcome common infections caused by E. coli.
Department of Biology Faculty of Medicine Masaryk University Brno Czech Republic
Faculty of Informatics Masaryk University Brno Czech Republic
RECETOX Center Faculty of Science Masaryk University Brno Czech Republic
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Rhouma M, Fairbrother JM, Beaudry F, Letellier A. 2017. Post weaning diarrhea in pigs: risk factors and non-colistin-based control strategies. Acta Vet Scand 59:31. 10.1186/s13028-017-0299-7. PubMed DOI PMC
Luppi A, Gibellini M, Gin T, Vangroenweghe F, Vandenbroucke V, Bauerfeind R, Bonilauri P, Labarque G, Hidalgo Á. 2016. Prevalence of virulence factors in enterotoxigenic Escherichia coli isolated from pigs with post-weaning diarrhoea in Europe. Porcine Health Manag 2:20. 10.1186/s40813-016-0039-9. PubMed DOI PMC
Fairbrother JM, Nadeau É, Gyles CL. 2005. Escherichia coli in postweaning diarrhea in pigs: an update on bacterial types, pathogenesis, and prevention strategies. Anim Health Res Rev 6:17–39. 10.1079/AHR2005105. PubMed DOI
Tseng M, Fratamico PM, Manning SD, Funk JA. 2014. Shiga toxin-producing Escherichia coli in swine: the public health perspective. Anim Health Res Rev 15:63–75. 10.1017/S1466252313000170. PubMed DOI PMC
Luppi A. 2017. Swine enteric colibacillosis: diagnosis, therapy and antimicrobial resistance. Porcine Health Manag 3:16. 10.1186/s40813-017-0063-4. PubMed DOI PMC
Sun Y, Kim SW. 2017. Intestinal challenge with enterotoxigenic Escherichia coli in pigs, and nutritional intervention to prevent postweaning diarrhea. Anim Nutr 3:322–330. 10.1016/j.aninu.2017.10.001. PubMed DOI PMC
Matise I, Sirinarumitr T, Bosworth BT, Moon HW. 2000. Vascular ultrastructure and DNA fragmentation in swine infected with Shiga toxin-producing Escherichia coli. Vet Pathol 37:318–327. 10.1354/vp.37-4-318. PubMed DOI
Casanova NA, Redondo LM, Dailoff GC, Arenas D, Fernández Miyakawa ME. 2018. Overview of the role of Shiga toxins in porcine edema disease pathogenesis. Toxicon 148:149–154. 10.1016/j.toxicon.2018.04.019. PubMed DOI
Bourgeois AL, Wierzba TF, Walker RI. 2016. Status of vaccine research and development for enterotoxigenic Escherichia coli. Vaccine 34:2880–2886. 10.1016/j.vaccine.2016.02.076. PubMed DOI
Majowicz SE, Scallan E, Jones-Bitton A, Sargeant JM, Stapleton J, Angulo FJ, Yeung DH, Kirk MD. 2014. Global incidence of human Shiga toxin-producing Escherichia coli infections and deaths: a systematic review and knowledge synthesis. Foodborne Pathog Dis 11:447–455. 10.1089/fpd.2013.1704. PubMed DOI PMC
Newell DG, La Ragione RM. 2018. Enterohaemorrhagic and other Shiga toxin-producing Escherichia coli (STEC): where are we now regarding diagnostics and control strategies? Transbound Emerg Dis 65:49–71. 10.1111/tbed.12789. PubMed DOI
Marshall BM, Levy SB. 2011. Food animals and antimicrobials: impacts on human health. Clin Microbiol Rev 24:718–733. 10.1128/CMR.00002-11. PubMed DOI PMC
Maron DF, Smith TJS, Nachman KE. 2013. Restrictions on antimicrobial use in food animal production: an international regulatory and economic survey. Global Health 9:48. 10.1186/1744-8603-9-48. PubMed DOI PMC
EMA Committee for Medicinal Products for Veterinary Use, EFSA Panel on Biological Hazards, Murphy D, Ricci A, Auce Z, Beechinor JG, Bergendahl H, Breathnach R, Bureš J, Duarte Da Silva JP, Hederová J, Hekman P, Ibrahim C, Kozhuharov E, Kulcsár G, Lander Persson E, Lenhardsson JM, Mačiulskis P, Malemis I, Markus‐Cizelj L, Michaelidou-Patsia A, Nevalainen M, Pasquali P, Rouby J-C, Schefferlie J, Schlumbohm W, Schmit M, Spiteri S, Srčič S, Taban L, Tiirats T, Urbain B, Vestergaard E, Wachnik-Święcicka A, Weeks J, Zemann B, Allende A, Bolton D, Chemaly M, Fernandez Escamez PS, Girones R, Herman L, Koutsoumanis K, Lindqvist R, Nørrung B, Robertson L, Ru G, Sanaa M, Simmons M, Skandamis P, Snary E, Speybroeck N, et al. 2017. EMA and EFSA joint scientific opinion on measures to reduce the need to use antimicrobial agents in animal husbandry in the European Union, and the resulting impacts on food safety (RONAFA). EFSA J 15:e04666. 10.2903/j.efsa.2017.4666. PubMed DOI PMC
Bosák J, Hrala M, Micenková L, Šmajs D. 2021. Non-antibiotic antibacterial peptides and proteins of Escherichia coli: efficacy and potency of bacteriocins. Expert Rev Anti Infect Ther 19:309–322. 10.1080/14787210.2020.1816824. PubMed DOI
Gillor O, Kirkup BC, Riley MA. 2004. Colicins and microcins: the next generation antimicrobials. Adv Appl Microbiol 54:129–146. 10.1016/S0065-2164(04)54005-4. PubMed DOI
Meade E, Slattery MA, Garvey M. 2020. Bacteriocins, potent antimicrobial peptides and the fight against multi drug resistant species: resistance is futile? Antibiotics (Basel) 9:32. 10.3390/antibiotics9010032. PubMed DOI PMC
Quigley EMM. 2019. Prebiotics and probiotics in digestive health. Clin Gastroenterol Hepatol 17:333–344. 10.1016/j.cgh.2018.09.028. PubMed DOI
Collado M, Isolauri E, Salminen S, Sanz Y. 2009. The impact of probiotic on gut health. Curr Drug Metab 10:68–78. 10.2174/138920009787048437. PubMed DOI
Schroeder B, Duncker S, Barth S, Bauerfeind R, Gruber AD, Deppenmeier S, Breves G. 2006. Preventive effects of the probiotic Escherichia coli strain Nissle 1917 on acute secretory diarrhea in a pig model of intestinal infection. Dig Dis Sci 51:724–731. 10.1007/s10620-006-3198-8. PubMed DOI
Krause DO, Bhandari SK, House JD, Nyachoti CM. 2010. Response of nursery pigs to a synbiotic preparation of starch and an anti-Escherichia coli K88 probiotic. Appl Environ Microbiol 76:8192–8200. 10.1128/AEM.01427-10. PubMed DOI PMC
Cascales E, Buchanan SK, Duché D, Kleanthous C, Lloubès R, Postle K, Riley M, Slatin S, Cavard D. 2007. Colicin biology. Microbiol Mol Biol Rev 71:158–229. 10.1128/MMBR.00036-06. PubMed DOI PMC
Duquesne S, Destoumieux-Garzón D, Peduzzi J, Rebuffat S. 2007. Microcins, gene-encoded antibacterial peptides from enterobacteria. Nat Prod Rep 24:708–734. 10.1039/b516237h. PubMed DOI
Micenková L, Bosák J, Štaudová B, Kohoutová D, Čejková D, Woznicová V, Vrba M, Ševčíková A, Bureš J, Šmajs D. 2016. Microcin determinants are associated with B2 phylogroup of human fecal Escherichia coli isolates. Microbiologyopen 5:490–498. 10.1002/mbo3.345. PubMed DOI PMC
Bosák J, Hrala M, Pirková V, Micenková L, Čížek A, Smola J, Kučerová D, Vacková Z, Budinská E, Koláčková I, Šmajs D. 2019. Porcine pathogenic Escherichia coli strains differ from human fecal strains in occurrence of bacteriocin types. Vet Microbiol 232:121–127. 10.1016/j.vetmic.2019.04.003. PubMed DOI
Setia A, Bhandari SK, House JD, Nyachoti CM, Krause DO. 2009. Development and in vitro evaluation of an Escherichia coli probiotic able to inhibit the growth of pathogenic Escherichia coli K88. J Anim Sci 87:2005–2012. 10.2527/jas.2008-1400. PubMed DOI
Bhandari SK, Opapeju FO, Krause DO, Nyachoti CM. 2010. Dietary protein level and probiotic supplementation effects on piglet response to Escherichia coli K88 challenge: performance and gut microbial population. Livest Sci 133:185–188. 10.1016/j.livsci.2010.06.060. DOI
Khafipour E, Munyaka PM, Nyachoti CM, Krause DO, Rodriguez-Lecompte JC. 2014. Effect of crowding stress and Escherichia coli K88+ challenge in nursery pigs supplemented with anti-Escherichia coli K88+ probiotics. J Anim Sci 92:2017–2029. 10.2527/jas.2013-7043. PubMed DOI
Salajka E, Salajkova Z, Alexa P, Hornich M. 1992. Colonization factor different from K88, K99, F41 and 987P in enterotoxigenic Escherichia coli strains isolated from postweaning diarrhoea in pigs. Vet Microbiol 32:163–175. 10.1016/0378-1135(92)90103-z. PubMed DOI
Dubreuil JD, Isaacson RE, Schifferli DM. 8 September 2016, posting date. Animal enterotoxigenic Escherichia coli. EcoSal Plus 2016 10.1128/ecosalplus.ESP-0006-2016. PubMed DOI PMC
Luise D, Lauridsen C, Bosi P, Trevisi P. 2019. Methodology and application of Escherichia coli F4 and F18 encoding infection models in post-weaning pigs. J Anim Sci Biotechnol 10:53. 10.1186/s40104-019-0352-7. PubMed DOI PMC
Wasteson Y. 2001. Zoonotic Escherichia coli. Acta Vet Scand Suppl 95:79–84. PubMed
Kaufmann M, Zweifel C, Blanco M, Blanco JE, Blanco J, Beutin L, Stephan R. 2006. Escherichia coli O157 and non-O157 Shiga toxin-producing Escherichia coli in fecal samples of finished pigs at slaughter in Switzerland. J Food Prot 69:260–266. 10.4315/0362-028x-69.2.260. PubMed DOI
Stahl CH, Callaway TR, Lincoln LM, Lonergan SM, Genovese KJ. 2004. Inhibitory activities of colicins against Escherichia coli strains responsible for postweaning diarrhea and edema disease in swine. Antimicrob Agents Chemother 48:3119–3121. 10.1128/AAC.48.8.3119-3121.2004. PubMed DOI PMC
Pilsl H, Šmajs D, Braun V. 1999. Characterization of colicin S4 and its receptor, OmpW, a minor protein of the Escherichia coli outer membrane. J Bacteriol 181:3578–3581. 10.1128/JB.181.11.3578-3581.1999. PubMed DOI PMC
Šmajs D, Weinstock GM. 2001. The iron- and temperature-regulated cjrBC genes of Shigella and enteroinvasive Escherichia coli strains code for colicin Js uptake. J Bacteriol 183:3958–3966. 10.1128/JB.183.13.3958-3966.2001. PubMed DOI PMC
Šmajs D, Weinstock GM. 2001. Genetic organization of plasmid ColJs, encoding colicin Js activity, immunity, and release genes. J Bacteriol 183:3949–3957. 10.1128/JB.183.13.3949-3957.2001. PubMed DOI PMC
Bosák J, Micenková L, Doležalová M, Šmajs D. 2016. Colicins U and Y inhibit growth of Escherichia coli strains via recognition of conserved OmpA extracellular loop 1. Int J Med Microbiol 306:486–494. 10.1016/j.ijmm.2016.07.002. PubMed DOI
Schamberger GP, Phillips RL, Jacobs JL, Diez-Gonzalez F. 2004. Reduction of Escherichia coli O157:H7 populations in cattle by addition of colicin E7-producing E. coli to feed. Appl Environ Microbiol 70:6053–6060. 10.1128/AEM.70.10.6053-6060.2004. PubMed DOI PMC
Budič M, Rijavec M, Petkovšek Ž, Žgur-Bertok D. 2011. Escherichia coli bacteriocins: antimicrobial efficacy and prevalence among isolates from patients with bacteraemia. PLoS One 6:e28769. 10.1371/journal.pone.0028769. PubMed DOI PMC
Mazurek-Popczyk J, Pisarska J, Bok E, Baldy-Chudzik K. 2020. Antibacterial activity of bacteriocinogenic commensal Escherichia coli against zoonotic strains resistant and sensitive to antibiotics. Antibiotics (Basel) 9:411–413. 10.3390/antibiotics9070411. PubMed DOI PMC
Šmajs D, Pilsl H, Braun V. 1997. Colicin U, a novel colicin produced by Shigella boydii. J Bacteriol 179:4919–4928. 10.1128/jb.179.15.4919-4928.1997. PubMed DOI PMC
Riley MA, Cadavid L, Collett MS, Neely MN, Adams MD, Phillips CM, Neel JV, Friedman D. 2000. The newly characterized colicin Y provides evidence of positive selection in pore-former colicin diversification. Microbiology 146:1671–1677. 10.1099/00221287-146-7-1671. PubMed DOI
Šmajs D, Matějková P, Weinstock GM. 2006. Recognition of pore-forming colicin Y by its cognate immunity protein. FEMS Microbiol Lett 258:108–113. 10.1111/j.1574-6968.2006.00201.x. PubMed DOI
Šmajs D, Doležalová M, Macek P, Žídek L. 2008. Inactivation of colicin Y by intramembrane helix-helix interaction with its immunity protein. FEBS J 275:5325–5331. 10.1111/j.1742-4658.2008.06662.x. PubMed DOI
Carlos C, Pires MM, Stoppe NC, Hachich EM, Sato MIZ, Gomes TAT, Amaral LA, Ottoboni LMM. 2010. Escherichia coli phylogenetic group determination and its application in the identification of the major animal source of fecal contamination. BMC Microbiol 10:161. 10.1186/1471-2180-10-161. PubMed DOI PMC
Micenková L, Bosák J, Vrba M, Ševčíková A, Šmajs D. 2016. Human extraintestinal pathogenic Escherichia coli strains differ in prevalence of virulence factors, phylogroups, and bacteriocin determinants. BMC Microbiol 16:218. 10.1186/s12866-016-0835-z. PubMed DOI PMC
Gordon DM, Cowling A. 2003. The distribution and genetic structure of Escherichia coli in Australian vertebrates: host and geographic effects. Microbiology 149:3575–3586. 10.1099/mic.0.26486-0. PubMed DOI
Scaldaferri F, Gerardi V, Mangiola F, Lopetuso LR, Pizzoferrato M, Petito V, Papa A, Stojanovic J, Poscia A, Cammarota G, Gasbarrini A. 2016. Role and mechanisms of action of Escherichia coli Nissle 1917 in the maintenance of remission in ulcerative colitis patients: an update. World J Gastroenterol 22:5505–5511. 10.3748/wjg.v22.i24.5505. PubMed DOI PMC
Cordonnier C, Thévenot J, Etienne-Mesmin L, Alric M, Livrelli V, Blanquet-Diot S. 2017. Probiotic and enterohemorrhagic Escherichia coli: an effective strategy against a deadly enemy? Crit Rev Microbiol 43:116–132. 10.1080/1040841X.2016.1185602. PubMed DOI
Cutler SA, Lonergan SM, Cornick N, Johnson AK, Stahl CH. 2007. Dietary inclusion of colicin E1 is effective in preventing postweaning diarrhea caused by F18-positive Escherichia coli in pigs. Antimicrob Agents Chemother 51:3830–3835. 10.1128/AAC.00360-07. PubMed DOI PMC
Sato T, Hamabata T, Takita E, Matsui T, Sawada K, Imaoka T, Nakanishi N, Nakayama K, Tsukahara T. 2017. Improved porcine model for Shiga toxin-producing Escherichia coli infection by deprivation of colostrum feeding in newborn piglets. Anim Sci J 88:826–831. 10.1111/asj.12769. PubMed DOI
Wang J, Ji H, Wang S, Liu H, Zhang W, Zhang D, Wang Y. 2018. Probiotic Lactobacillus plantarum promotes intestinal barrier function by strengthening the epithelium and modulating gut microbiota. Front Microbiol 9:1953. 10.3389/fmicb.2018.01953. PubMed DOI PMC
Cheng MP, Domingo MC, Lévesque S, Yansouni CP. 2016. A case report of a deep surgical site infection with Terrisporobacter glycolicus/T. mayombei and review of the literature. BMC Infect Dis 16:529. 10.1186/s12879-016-1865-8. PubMed DOI PMC
Burrough ER, Arruda BL, Plummer PJ. 2017. Comparison of the luminal and mucosa-associated microbiota in the colon of pigs with and without swine dysentery. Front Vet Sci 4:139. 10.3389/fvets.2017.00139. PubMed DOI PMC
Kiros TG, Derakhshani H, Pinloche E, D’Inca R, Marshall J, Auclair E, Khafipour E, Van Kessel A. 2018. Effect of live yeast Saccharomyces cerevisiae (Actisaf Sc 47) supplementation on the performance and hindgut microbiota composition of weanling pigs. Sci Rep 8:5315. 10.1038/s41598-018-23373-8. PubMed DOI PMC
Šmajs D, Bureš J, Šmarda J, Chaloupková E, Květina J, Förstl M, Kohoutová D, Kuneš M, Rejchrt S, Lesná J, Kopáčová M. 2012. Experimental administration of the probiotic Escherichia coli strain Nissle 1917 results in decreased diversity of E. coli strains in pigs. Curr Microbiol 64:205–210. 10.1007/s00284-011-0051-x. PubMed DOI
Suzzi G, Tofalo R, Golí N, Veljoví K, Diní M, Lukí J, Mihajloví S, Tolinački M, Tolinački T, Živkoví M, Begoví J, Mrvaljeví I, Terzí C-Vidojeví A. 2017. Promotion of early gut colonization by probiotic intervention on microbiota diversity in pregnant sows. Front Microbiol 8:2028. 10.3389/fmicb.2017.02028. PubMed DOI PMC
Shin D, Chang SY, Bogere P, Won KH, Choi JY, Choi YJ, Lee HK, Hur J, Park BY, Kim Y, Heo J. 2019. Beneficial roles of probiotics on the modulation of gut microbiota and immune response in pigs. PLoS One 14:e0220843. 10.1371/journal.pone.0220843. PubMed DOI PMC
Clermont O, Bonacorsi S, Bingen E. 2000. Rapid and simple determination of the Escherichia coli phylogenetic group. Appl Environ Microbiol 66:4555–4558. 10.1128/aem.66.10.4555-4558.2000. PubMed DOI PMC
Zajacova ZS, Konstantinova L, Alexa P. 2012. Detection of virulence factors of Escherichia coli focused on prevalence of EAST1 toxin in stool of diarrheic and non-diarrheic piglets and presence of adhesion involving virulence factors in astA positive strains. Vet Microbiol 154:369–375. 10.1016/j.vetmic.2011.07.029. PubMed DOI
Šmarda J. 1963. Lysogenie a colicinogenie bakterií Escherichia coli. PhD thesis. Masaryk University, Brno, Czech Republic.
Šmarda J, Obdržálek V. 1966. Colicine Q. Zentralbl Bakteriol Orig 200:493–497. PubMed
Šmarda J, Šmajs D. 1998. Colicins—exocellular lethal proteins of Escherichia coli. Folia Microbiol 43:563–582. 10.1007/BF02816372. PubMed DOI
Alexa P, Rychlík I, Nejezchleb A, Hamřík J. 1997. Identification of enterotoxin-producing strains of Escherichia coli by PCR and biological methods. Vet Med (Praha) 42:97–100. PubMed
Bosák J, Micenková L, Vrba M, Ševčíková A, Dědičová D, Garzetti D, Šmajs D. 2013. Unique activity spectrum of colicin FY: all 110 characterized Yersinia enterocolitica isolates were colicin FY susceptible. PLoS One 8:e81829. 10.1371/journal.pone.0081829. PubMed DOI PMC
Patzer SI, Baquero MR, Bravo D, Moreno F, Hantke K. 2003. The colicin G, H and X determinants encode microcins M and H47, which might utilize the catecholate siderophore receptors FepA, Cir, Fiu and IroN. Microbiology 149:2557–2570. 10.1099/mic.0.26396-0. PubMed DOI
Eraso JM, Chidambaram M, Weinstock GM. 1996. Increased production of colicin E1 in stationary phase. J Bacteriol 178:1928–1935. 10.1128/jb.178.7.1928-1935.1996. PubMed DOI PMC
Kuhar I, Žgur-Bertok D. 1999. Transcription regulation of the colicin K cka gene reveals induction of colicin synthesis by differential responses to environmental signals. J Bacteriol 181:7373–7380. 10.1128/JB.181.23.7373-7380.1999. PubMed DOI PMC
Moreno F, Gónzalez-Pastor JE, Baquero MR, Bravo D. 2002. The regulation of microcin B, C and J operons. Biochimie 84:521–529. 10.1016/S0300-9084(02)01452-9. PubMed DOI
Trckova M, Lorencova A, Hazova K, Sramkova Zajacova Z. 2016. Prophylaxis of post-weaning diarrhoea in piglets by zinc oxide and sodium humate. Vet Med (Praha) 60:351–360. 10.17221/8382-VETMED. DOI
Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. 10.1093/bioinformatics/btu170. PubMed DOI PMC
Aronesty E. 2011. Command-line tools for processing biological sequencing data. https://expressionanalysis.github.io/ea-utils/.
Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–2461. 10.1093/bioinformatics/btq461. PubMed DOI
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pe˜a AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336. 10.1038/nmeth.f.303. PubMed DOI PMC
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. 2013. The SILVA ribosomal RNA gene database project: improved data processing and Web-based tools. Nucleic Acids Res 41:D590–D596. 10.1093/nar/gks1219. PubMed DOI PMC
Gentleman R. 2008. R programming for bioinformatics. CRC Press, Boca Raton, FL.
R Core Team. 2019. R: the R project for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.r-project.org/.
Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, Minchin PR, O’Hara RB, Simpson GL, Solymos P, Stevens MHH, Szoecs E, Wagner H. 2017. Vegan: community ecology package. R package version 2.4-3. https://cran.r-project.org/web/packages/vegan/index.html.
Wickham H. 2016. ggplot2: elegant graphics for data analysis. Springer-Verlag, New York, NY.
Complete genome sequences of five Escherichia coli strains with probiotic attributes