As Potential Probiotics : Status , Concerns , and Future Perspectives. *Front. Microbiol.* 8, 1490. doi:10.3389/fmicb.2017.01490.

EMA (2015). European public MRL assessment report ( EPMAR ). United Kingdom.

Er, S., Koparal, A. T., and Kivanç, M. (2015). Cytotoxic effects of various lactic acid bacteria on Caco-2 cells. *Turkish J. Biol.* 39, 23–30. doi:10.3906/biy-1402-62.

ESVAC (2017). Sales of veterinary antimicrobial agents in 30 European countries in 2015 Trends from 2010 to 2015 (EMA/184855/2017).

Ewaschuk, J. B., Diaz, H., Meddings, L., Diederichs, B., Dmytrash, A., Backer, J., et al. (2008). Secreted bioactive factors from Bifidobacterium infantis enhance epithelial cell barrier function. *Am. J. Physiol. Liver Physiol.* 295, 1025–1034. doi:10.1152/ajpgi.90227.2008.

Ezema (2013). Probiotics in animal production : A review. *J. Vet. Med. Anim. Heal.* 5, 308–316. doi:10.5897/JVMAH2013.0201.

FAO/OMS (2002). Guidelines for the Evaluation of Probiotics in Food. doi:10.1111/j.1469-0691.2012.03873.

FAO (2016a). *Probiotics in animal nutrition – Production, impact and regulation.* , ed. Harinder P.S. Makkar FAO Animal Production and Health Paper No. 179. Rome doi:10.3920/BM2008.1002.

FAO (2016b). The FAO Action Plan on Antimicrobial Resistance. Rome.

Farrell, D. (2012). The role of poultry in human nutrition. Available at: http://www.fao.org/docrep/013/al709e/al709e00.pdf.

Fasina, Y. O., and Lillehoj, H. S. (2018). Characterization of intestinal immune response to *Clostridium perfringens* infection in broiler chickens. *Poult. Sci.* 0, 1–11. doi:10.3382/ps/pey390.

FDA (2016). Antimicrobials Sold or Distributed for Use in Food-Producing Animals.

Felis, G. E., and Dellaglio, F. (2007). Taxonomy of Lactobacilli and Bifidobacteria. *Curr. Issues Intest. Microbiol.* 8, 44–61.

Ferket, P. R. (2006). Incubation and in ovo nutrition affects neonatal development. in *33rd Annual Carolina Poultry Nutrition Conference*.

Fernández, L., Álvarez-ortega, C., Wiegand, I., Olivares, J., Kocíncová, D., Lam, J. S., et al. (2013). Characterization of the polymyxin B resistome of *Pseudomonas aeruginosa*. *Antimicrob. Agents Chemother.* 57, 110–119. doi:10.1128/AAC.01583-12.

Filazi, A., Yurdakok-dikmen, B., Kuzukiran, O., and Sireli, U. T. (2017). “Mycotoxins in Poultry,” in *Poultry Science* (Milad Manafi, IntechOpen). doi:10.5772/66302.

Fonseca, F., Cenard, S., and Passot, S. (2015). *Cryopreservation and Freeze-Drying Protocols, Methods in Molecular Biology* , eds. W. F. Wolkers and H. Oldenhof Springer Science+Business Media New York 2015 doi:10.1007/978-1-4939-2193-5.

Food and Agriculture Organisation (2018). Meat Market Review. *Meat Mark. Rev.* , 1–11. Available at: http://www.fao.org/3/I9286EN/i9286en.pdf.

Food and Veterinary Office (2015). Residue monitoring for critically important antimicrobials. Luxembourg doi:10.2875/858963.

Fowler, J., Kakani, R., Haq, A., Byrd, J. A., and Bailey, C. A. (2015). Growth promoting effects of prebiotic yeast cell wall products in starter broilers under an immune stress and *Clostridium perfringens* challenge.

Friedrich, U., and Lenke, J. (2006). Improved enumeration of lactic acid bacteria in mesophilic dairy starter cultures by using multiplex quantitative real-time PCR and flow cytometry-florescence in situ hybridization. *Appl. Environ. Microbiol.* 72, 4163–4171.
doi:10.1128/AEM.02283-05.

Fuller, R. (1989). Probiotics in man and animals. *J. Appl. Bacteriol.* 66, 365-378.

Fuller, R. (1992). "History and development of probiotics," in *Probiotics: The scientific basis* (Dordrecht: Springer Netherlands), 1-8. doi:10.1007/978-94-011-2364-8_1.

Gaffga, N. H., Behravesh, C. B., Ettestad, P. J., Smelser, C. B., Rhorer, A. R., Cronquist, A. B., et al. (2012). Outbreak of Salmonellosis Linked to Live Poultry from a Mail-Order Hatchery. *N. Engl. J. Med.* 366, 2065-2073.

Gaggìa, F., Mattarelli, P., and Biavati, B. (2010). Probiotics and prebiotics in animal feeding for safe food production. *Int. J. Food Microbiol.* 141, S15-S28. doi:10.1016/j.ijfoodmicro.2010.02.031.

Gänzle, M., and Gobbetti, M. (2013). "Physiology and Biochemistry of Lactic Acid Bacteria," in *Handbook on Sourdough Biotechnology*, eds. M. Gänzle and M. Gobbetti (Springer Science+Business Media New York), 183-216. doi:10.1007/978-1-4614-5425-0.

Garde, S., Gómez-Torres, N., Hernández, M., and Ávila, M. (2014). Susceptibility of *Clostridium perfringens* to antimicrobials produced by lactic acid bacteria: Reuterin and nisin. *Food Control* 44, 22-25. doi:10.1016/j.foodcont.2014.03.034.

Gasbarrini, G., and Bonvicini, F. (2016). Probiotics History. *J. Clin. Gastroenterol.* 50, S116-119. doi:10.1097/MCG.0000000000000697.

Geier, M. S., Mikkelsen, L. L., Torok, V. A., Allison, G. E., Olnood, C. G., and Boulianne, M. (2010). Comparison of alternatives to in-feed antimicrobials for the prevention of clinical necrotic enteritis. *J. Appl. Microbiol.* 109, 1329-1338. doi:10.1111/j.1365-2672.2010.04758.x.

Gérard, P., Brézillon, C., Quéré, F., Salmon, A., and Rabot, S. (2008). Characterization of Cecal Microbiota and Response to an Orally Administered *Lactobacillus* Probiotic Strain in the Broiler Chicken. *J. Mol. Microbiol. Biotechnol.* 14, 115-122. doi:10.1159/000106090.

Gerhardt, P., Murray, R. G. E., Wood, W. A., and Krieg, N. R. (1994). *Methods for General and Molecular Bacteriology*. Washington, D. C.: American Society for Microbiology.

Ghaffar, T., Irshad, M., Anwar, Z., Aqil, T., Zulifqar, Z., Tariq, A., et al. (2014). Recent trends in lactic acid biotechnology: A brief review on production to purification. *J. Radiat. Res. Appl. Sci.* 7, 222-229. doi:10.1016/j.jrras.2014.03.002.

Giesecke, J., and McCarthy, N. (2001). Incidence of Guillain-Barré Syndrome following Infection with *Campylobacter jejuni*. *Am. J. Epidemiol.* 153, 610-614. doi:10.1093/aje/153.6.610.

GLEAM2.0. (2018). Global Livestock Environmental Assessment Model.

Goh, Y. J., and Klaenhammer, T. R. (2010). Functional roles of aggregation-promoting-like factor in stress tolerance and adherence of *Lactobacillus acidophilus* NCFM. *Appl. Environ. Microbiol.* 76, 5005-5012. doi:10.1128/AEM.00030-10.

Golic, N., Veljovi, K., Popovi, N., Djoki, J., Strahini, I., Mrvaljevi, I., et al. (2017). *In vitro* and *in vivo* antagonistic activity of new probiotic culture against *Clostridium difficile* and *Clostridium perfringens*. *BMC Microbiol.* 17. doi:10.1186/s12866-017-1015-5.

Gomaa, E. Z. (2013). Antimicrobial and anti-adhesive properties of biosurfactant produced by lactobacilli isolates, biofilm formation and aggregation ability. *J. Gen. Appl. Microbiol.* 59, 425-436. doi:10.2323/jgam.59.425.

Gómez, N. C., Ramiro, J. M. P., Quecan, B. X. V., and de Melo Franco, B. D. G. (2016). Use of potential probiotic lactic acid bacteria (LAB) biofilms for the control of Listeria monocytogenes, *Salmonella Typhimurium*, and *Escherichia coli* O157:H7 biofilms formation. *Front. Microbiol.* 7, 863. doi:10.3389/fmicb.2016.00863.
Gong, J., Forster, R. J., Yu, H., Chambers, J. R., Wheatcroft, R., Sabour, P. M., et al. (2002). Molecular analysis of bacterial populations in the ileum of broiler chickens and comparison with bacteria in the cecum. *FEMS Microbiol. Ecol.* 41, 171–179.

Gonzalez-Rodriguez, I., Ruiz, L., Gueimonde, M., Margolles, A., and Sanchez, B. (2013). Factors involved in the colonization and survival of bifidobacteria in the gastrointestinal tract. *FEMS Microbiol. Lett.* 340, 1–10. doi:10.1111/1574-6968.12056.

Gould, L. H., and Limbago, B. (2010). *Clostridium difficile* in Food and Domestic Animals: A New Foodborne Pathogen? *Clin. Infect. Dis.* 51, 577–582. doi:10.1086/655692.

Gouriet, F., Million, M., Henri, M., Fournier, P., and Raoult, D. (2012). *Lactobacillus rhamnosus* bacteremia: an emerging clinical entity. *Eur. J. Clin. Microbiol. Infect. Dis.* 31, 2469–2480. doi:10.1007/s10096-012-1599-5.

Granato, D., Perotti, F., Masserey, I., Rouvet, M., Golliard, M., Servin, A., et al. (1999). Cell Surface-Associated Lipoteichoic Acid Acts as an Adhesion Factor for Attachment of *Lactobacillus johnsonii* La1 to Human Enterocyte-Like Caco-2 Cells. *Appl. Environ. Microbiol.* 65, 1071–1077.

Grande Burgos, M., Pulido, R., del Carmen López Aguayo, M., Gálvez, A., and Lucas, R. (2014). The cyclic antibacterial peptide enterocin AS-48: Isolation, mode of action, and possible food applications. *Int. J. Mol. Sci.* 15, 22706–22727. doi:10.3390/ijms151222706.

Grant, A., Hashem, F., and Parveen, S. (2016). *Salmonella* and *Campylobacter*: Antimicrobial resistance and bacteriophage control in poultry. *Food Microbiol.* 53, 104–109. doi:10.1016/j.fm.2015.09.008.

Grazul, H., Kanda, L. L., and Gondek, D. (2016). Impact of probiotic supplements on microbiome diversity following antibiotic treatment of mice. *Gut Microbes* 7, 101–114. doi:10.1080/19490976.2016.1138197.

Gross, G., Snel, J., Boekhorst, J., Smits, M. A., and Kleerebezem, M. (2010). Biodiversity of mannose-specific adhesion in *Lactobacillus plantarum* revisited: strain-specific domain composition of the mannose-adhesin. *Benef. Microbes* 1, 61–66. doi:10.3920/BM2008.1006.

Gueimonde, M., Flórez, A. B., Reyes-gavilán, C. G. D. L., Margolles, A., Microbiología, D. De, Lácteos, D. P., et al. (2009). Intrinsic resistance in lactic acid bacteria and bifidobacteria: the role of multidrug resistance transporters. *Int. J. Probiotics Prebiotics* 4, 181–186.

Gueimonde, M., Sánchez, B., de los Reyes-Gavilán, C. G., and Margolles, A. (2013). Antibiotic resistance in probiotic bacteria. *Front. Microbiol.* 4, 1–6. doi:10.3389/fmicb.2013.00202.

Guo, S., Liu, D., Zhang, B., Li, Z., Li, Y., Ding, B., et al. (2017). Two *Lactobacillus* species inhibit the growth and α-toxin production of *Clostridium perfringens* and induced proinflammatory factors in chicken intestinal epithelial cells in vitro. *Front. Microbiol.* 8, 2081. doi:10.3389/fmicb.2017.02081.

Gupta, R. S., and Gao, B. (2009). Phylogenomic analyses of clostridia and identification of novel protein signatures that are specific to the genus *Clostridium* sensu stricto (cluster I). *Int. J. Syst. Evol. Microbiol.* 59, 285–294. doi:10.1099/ijs.0.001792-0.

Hai, N. V. (2015). The use of probiotics in aquaculture. *J. Appl. Microbiol.* 119, 917–935. doi:10.1111/jam.12886.

Hamilton-Miller, J. M. T., and Shah, S. (1998). Vancomycin susceptibility as an aid to the identification of lactobacilli. *Lett. Appl. Microbiol.* 26, 153–154. doi:10.1046/j.1472-765X.1998.00297.x.

Han, F.-F., Liu, Y.-F., Xie, Y.-G., Gao, Y.-H., Luan, C., and Wang, Y.-Z. (2011). Antimicrobial peptides derived from different animals: comparative studies of antimicrobial properties,
cytotoxicity and mechanism of action. *World J. Microbiol. Biotechnol.* 27, 1847-1857.
doi:10.1007/s11274-010-0643-9.

Han, S. K., and Shin, H. S. (2004). Biohydrogen production by anaerobic fermentation of food waste. *Int. J. Hydrogen Energy* 29, 569-577. doi:10.1016/j.ijhydene.2003.09.001.

Hancock, R. E. W., and Scott, M. G. (2000). The role of antimicrobial peptides in animal defenses. *PNAS* 97, 8856-8861. doi:10.1073/pnas.97.16.8856.

Handwerger, S., Pucci, M. J., Volk, K. J., Liu, J., and Lee, M. S. (1994). Vancomycin-Resistant *Leuconostoc mesenteroides* and *Lactobacillus*. *J. Bacteriol*. 176, 260-264.

Hao, Y., Gu, X. H., and Wang, X. L. (2012). Overexpression of heat shock protein 70 and its relationship to intestine under acute heat stress in broilers : 1 . Intestinal structure and digestive function. *Poult. Sci.* 91, 781-789.

Hardy, H., Harris, J., Lyon, E., Beal, J., and Foey, A. D. (2013). Probiotics, prebiotics and immunomodulation of gut mucosal defences: Homeostasis and immunopathology. *Nutrients* 5, 1869-1912. doi:10.3390/nu5061869.

Hartemink, R., Domenech, V. R., and Rombouts, F. M. (1997). Methods LAMVAB — A new selective medium for the isolation of lactobacilli from faeces. 29, 77-84.

Harvey, R. B., Norman, K. N., Andrews, K., Hume, M. E., Scanlan, C. M., Callaway, T. R., et al. (2011). *Clostridium difficile* in Poultry and Poultry Meat. *Foodborne Pathog. Dis.* 8, 1321-1323. doi:10.1089/fpd.2011.0936.

Hermans, P., and Morgan, K. (2007). Prevalence and associated risk factors of necrotic enteritis on broiler farms in the United Kingdom; a cross-sectional survey. *Avian Pathol.* 36, 43-51.

Hibberd, P. L., and Davidson, L. (2008). Probiotic Foods and Drugs : Impact of US Regulatory Status on Design of Clinical Trials. *Clin. Infect. Dis.* 1, S137-40. doi:10.1086/523321.

Hoelzer, K., Bielke, L., Blake, D. P., Cox, E., Cutting, S. M., Devriendt, B., et al. (2018a). Vaccines as alternatives to antibiotics for food producing animals. Part 1: Challenges and needs. *Vet. Res.* 49, 64. doi:10.1186/s13567-018-0560-8.

Hoelzer, K., Bielke, L., Blake, D. P., Cox, E., Cutting, S. M., Devriendt, B., et al. (2018b). Vaccines as alternatives to antibiotics for food producing animals. Part 2: new approaches and potential solutions. *Vet. Res.* 49, 70. doi:10.1186/s13567-018-0560-8.

Hoerr, F. J. (2010). Clinical aspects of immunosuppression in poultry. *Avian Dis.* 54, 91-99.
doi:10.2298/VETGL1502091R.

Hofacre, C. L., Smith, J. A., and Mathis, G. F. (2018). An optimist ’ s view on limiting necrotic enteritis and maintaining broiler gut health and performance in today ’ s marketing , food safety , and regulatory. *Poult. Sci.* 0, 1-5. doi:10.3382/ps/pey082/4945454.

Hofmann, A. F., and Eckmann, L. (2006). How bile acids confer gut mucosal protection against bacteria. *Proc. Natl. Acad. Sci.* 103, 4333-4334. doi:10.1073/pnas.0600780103.

Høiby, N., Bjarnsholt, T., Givskov, M., Molin, S., and Ciofu, O. (2010). International Journal of Antimicrobial Agents Antibiotic resistance of bacterial biofilms. *Int. J. Antimicrob. Agents* 35, 322-332. doi:10.1016/j.ijantimicag.2009.12.011.

Holzapfel, W. H. ., and Wood, B. J. B. (1995). *The Genera of Lactic Acid Bacteria*. Springer-S. eds. B. J. B. Wood and W. H. Holzapfel Boston, MA: Springer US doi:10.1007/978-1-4615-5817-0.

Hong, Y. H., Dinh, H., Lillehoj, H. S., Song, K., and Oh, J. (2014). Differential regulation of microRNA transcriptome in chicken lines resistant and susceptible to necrotic enteritis disease. *Poult. Sci.* 93, 1383-1395. doi:10.3382/ps.2013-03666.

Hor, Y. Y., and Liong, M. T. (2014). Use of extracellular extracts of lactic acid bacteria and
bifidobacteria for the inhibition of dermatological pathogen *Staphylococcus aureus*. *Dermatologica Sin.* 32, 141-147. doi:10.1016/j.dsi.2014.03.001.

Howard, Z. R., O'Bryan, C. A., Crandall, P. G., and Ricke, S. C. (2012). *Salmonella Enteritidis* in shell eggs: Current issues and prospects for control. *Food Res. Int.* 45, 755-764. doi:10.1016/j.foodres.2011.04.030.

Hynönen, U., and Palva, A. (2013). *Lactobacillus* surface layer proteins: Structure, function and applications. *Appl. Microbiol. Biotechnol.* 97, 5225-5243. doi:10.1007/s00253-013-4962-2.

Immerseel, F. Van, Buck, J. De, Pasmans, F., Haesebrouck, F., Ducatelle, R., Immerseel, F. Van, et al. (2010). *Clostridium perfringens* in poultry: an emerging threat for animal and public health. *Avian Pathol.* 33, 537-549. doi:10.1080/03079450400013162.

Iowa State University (2016). Newcastle Disease.

Jang, S. I., Lillehoj, H. S., Lee, S., Lee, K. W., Lillehoj, E. P., Ho, Y., et al. (2013). Relative Disease Susceptibility and Clostridial Toxin Antibody Responses in Three Commercial Broiler Lines Coinfected with *Clostridium perfringens* and *Eimeria maxima* Using an Experimental Model of Necrotic Enteritis Research Note — Relative Disease Suscep. *Avian Dis.* 57, 684-687.

Jayaraman, S., Thangavel, G., Kurian, H., Mani, R., Mukkalil, R., and Chirakkal, H. (2018). *Bacillus subtilis* PB6 improves intestinal health of broiler chickens challenged with *Clostridium perfringens* -induced necrotic enteritis. *Poult. Sci.* 92, 370-374. doi:10.3382/ps.2012-02528.

Jin, L. Z., Ho, Y. W., Abdullah, N., and Jalaludin, S. (1998). Growth performance, intestinal microbial populations, and serum cholesterol of broilers fed diets containing *Lactobacillus* cultures. *Poult. Sci.* 77, 1259-1265. doi:10.1093/ps/77.9.1259.

Joerger, R. D. (2003). Alternatives to antibiotics: bacteriocins, antimicrobial peptides and bacteriophages. *Poult. Sci.* 82, 640-647. doi:10.1093/ps/82.4.640.

Johnson, R. P., Gyles, C. L., Huff, W. E., Ojha, S., Huff, G. R., Rath, N. C., et al. (2008). Bacteriophages for prophylaxis and therapy in cattle, poultry and pigs. *Anim. Heal. Res. Rev.* 9, 201-215. doi:10.1017/S1466252308001576.

Jones, S. E., and Versalovic, J. (2009). Probiotic *Lactobacillus reuteri* biofilms produce antimicrobial and anti-inflammatory factors. *BMC Microbiol.* 9, 1-9. doi:10.1186/1471-2180-9-35.

Joosten, H. M. L. J., and Nuñez, M. (1995). Adsorption of nisin and enterocin 4 to polypropylene and glass surfaces and its prevention by Tween 80. *Lett. Appl. Microbiol.* 21, 389-392. doi:10.1111/j.1472-765X.1995.tb01089.x.

Joyce, S. A., Macsharry, J., Casey, P. G., Kinsella, M., Murphy, E. F., and Shanahan, F. (2014). Regulation of host weight gain and lipid metabolism by bacterial bile acid modification in the gut. *PNAS* 111, 7421-7426. doi:10.1073/pnas.1323599111.

Juncioni de Arauz, L., Faustino Jozala, A., Gava Mazzola, P., and Vessoni Penna, T. C. (2009). Nisin biotechnological production and application: a review. *Trends Food Sci. Technol.* 20, 146-154. doi:10.1016/j.tifs.2009.01.056.

Kaakoush, N. O., Castaño-Rodríguez, N., Mitchell, H. M., and Man, S. M. (2015). Global Epidemiology of *Campylobacter* Infection. *Clin. Microbiol. Rev.* 28, 687-720. doi:10.1128/CMR.00006-15.

Kabir, S. M. L. (2009). The role of probiotics in the poultry industry. *Int. J. Mol. Sci.* 10, 3531-3546. doi:10.3390/ijms10083531.

Kanai, T., Mikami, Y., Hayashi, A., and Interleukin-, M. Á. (2015). A breakthrough in probiotics : *Clostridium butyricum* regulates gut homeostasis and anti-inflammatory response in
inflammatory bowel disease. *J. Gastroenterol.* 50, 928-939. doi:10.1007/s00535-015-1084-x.

Kang, M., Lim, H., Oh, J., Lim, Y., Wuertz-kozak, K., Harro, J. M., et al. (2017). Antimicrobial activity of *Lactobacillus salivarius* and *Lactobacillus fermentum* against *Staphylococcus aureus*. *Pathog. Dis.* 75, ftx009. doi:10.1093/femspd/ftx009.

Kariuki, S., Gordon, M. A., Feasey, N., and Parry, C. M. (2015). Antimicrobial resistance and management of invasive *Salmonella* disease. *Vaccine* 33, C21-C29. doi:10.1016/j.vaccine.2015.03.102.

Keessen, E. C., Gaastra, W., and Lipman, L. J. A. (2011). *Clostridium difficile* infection in humans and animals, differences and similarities. *Vet. Microbiol.* 153, 205-217. doi:10.1016/j.vetmic.2011.03.020.

Kers, J. G., Velkers, F. C., Fischer, E. A. J., Hermes, G. D. A., Stegeman, J. A., Smidt, H., et al. (2018). Host and environmental factors affecting the intestinal microbiota in chickens. *Front. Microbiol.* 9, 235. doi:10.3389/fmicb.2018.00235.

Keto-Timonen, R., Heikinheimo, A., Eerola, E., and Korkeala, H. (2006). Identification of *Clostridium* Species and DNA Fingerprinting of *Clostridium perfringens* by Amplified Fragment Length Polymorphism Analysis □. *J. Clin. Microbiol.* 44, 4057-4065. doi:10.1128/JCM.01275-06.

Keyburn, A. L., Bannam, T. L., Moore, R. J., and Rood, J. I. (2010). NetB, a Pore-Forming Toxin from Necrotic Enteritis Strains of *Clostridium perfringens*. 1913-1927. doi:10.3390/toxins2071913.

Keyburn, A. L., Boyce, J. D., Vaz, P., Bannam, T. L., Ford, M. E., Parker, D., et al. (2008). NetB, a new toxin that is associated with avian necrotic enteritis caused by *Clostridium perfringens*. *PLoS Pathog.* 4. doi:10.1371/journal.ppat.0040026.

Keyburn, A. L., Portela, R. W., Sproat, K., Ford, M. E., Bannam, T. L., Yan, X., et al. (2013). Vaccination with recombinant NetB toxin partially protects broiler chickens from necrotic enteritis. *Vet. Res.* 44, 1. doi:10.1186/1297-9716-44-54.

Keyburn, A. L., Sheedy, S. A., Ford, M. E., Williamson, M. M., Awad, M. M., Rood, J. I., et al. (2006). Alpha-Toxin of *Clostridium perfringens* Is Not an Essential Virulence Factor in Necrotic Enteritis in Chickens □. *Infect. Immun.* 74, 6496-6500. doi:10.1128/IAI.00806-06.

Khan, M. M. T., Pyle, B. H., and Camper, A. K. (2010). Specific and rapid enumeration of viable but nonculturable and viable-culturable gram-negative bacteria by using flow cytometry. *Appl. Environ. Microbiol.* 76, 5088-5096. doi:10.1128/AEM.02932-09.

Kiczorowska, B., Samolińska, W., Al-Yasiry, A. R. M., Kiczorowski, P., and Winiarska-Mieczan, A. (2017). The natural feed additives as immunostimulants in monogastric animal nutrition – a review. *Ann. Anim. Sci.* 17, 605-625. doi:10.1515/aoas-2016-0076.

Kim, D. H., and Austin, B. (2008). Characterization of probiotic carnobacteria isolated from rainbow trout (Oncorhynchus mykiss) intestine. *Lett. Appl. Microbiol.* 47, 141-147. doi:10.1111/j.1472-765X.2008.02401.x.

Kizerwetter-Świda, M., and Binek, M. (2009). Protective effect of potentially probiotic *Lactobacillus* strain on infection. *Polish J. Vet. Sci. Vol.* 12, 15-20.

Kizerwetter-Świda, M., and Binek, M. (2016). Assessment of potentially probiotic properties of *Lactobacillus* strains isolated from chickens. *Pol. J. Vet. Sci.* 19, 15-20. doi:10.1515/pjvs-2016-0003.

Klare, I., Konstabel, C., Werner, G., Huys, G., Vankerckhoven, V., Kahlmeter, G., et al. (2007). Antimicrobial susceptibilities of *Lactobacillus*, *Pediococcus* and *Lactococcus* human isolates
and cultures intended for probiotic or nutritional use. *J. Antimicrob. Chemother.* 59, 900–912.
doi:10.1093/jac/dkm035.

Knap, A. I., Lund, B., Kehlet, A. B., Hofacre, C., Mathis, G., Knap, I., et al. (2010). *Bacillus licheniformis* prevents necrotic enteritis in broiler chickens research. *Avian Dis.* 54, 931–935.
doi:10.1637/9106-101509-ResNote.1.

Kon, K., and Rai, M. (2016). *Antibiotic resistance. Mechanisms and New Antimicrobial Approaches*. , eds. K. Kon and M. Rai Academic Press doi:10.1016/B978-0-12-803642-6.00018-6.

Kondo, F., Tottori, J., and Soki, K. (1988). Ulcerative enteritis in broiler chickens caused by *Clostridium colinum* and *in vitro* activity of 19 antimicrobial agents in tests on isolates. *Poult. Sci.* 67, 1424–1430. doi:10.3382/ps.0671424.

Koransky, J. R., Stargel, M. D., and Dowell, V. R. (1979). *Clostridium septicum* bacteremia. Its clinical significance. *Am. J. Med.* 66, 63–66. doi:10.1016/0002-9343(79)90483-2.

Kos, B., J.Suskovic, Vukovic, S., Simpraga, M., Frece, J., and Matosic, S. (2003). Adhesion and aggregation ability of probiotic strain *Lactobacillus acidophilus* M92. *J. Appl. Microbiol.* 94, 981–987.

Koskenniemi, K., Laakso, K., Koponen, J., Kankainen, M., Greco, D., Auvinen, P., et al. (2011). Proteomics and Transcriptomics Characterization of Bile Stress Response in Probiotic *Lactobacillus rhamnosus* GG. *Mol. Cell. Proteomics* 10, M110.002741.
doi:10.1074/mcp.M110.002741.

Kregel, K. C. (2002). Heat shock proteins: modifying factors in physiological stress responses and acquired thermotolerance KEVIN. *J. Appl. Physiol.* 92, 2177–2186.

Kwok, S., Chang, S. Y., Sninsky, J. J., and Wang, A. (1994). A Guide to the Design and Use of Mismatched and Degenerate Primers. *PCR Methods Appl.* 3, S39-47.

La Ragione, R. M., Narbad, A., Gasson, M. J., and Woodward, M. J. (2004). *In vivo* characterization of *Lactobacillus johnsonii* FI9785 for use as a defined competitive exclusion agent against bacterial pathogens in poultry. *Lett. Appl. Microbiol.* 38, 197–205.
doi:10.1111/j.1472-765X.2004.01474.x.

La Ragione, R. M., and Woodward, M. J. (2003). Competitive exclusion by *Bacillus subtilis* spores of *Salmonella enterica* serotype Enteritidis and *Clostridium perfringens* in young chickens. *Vet. Microbiol.* 94, 245–256. doi:10.1016/S0378-1135(03)00077-4.

Lacey, J. A., Keyburn, A. L., Forda, M. E., Portela, R. W., Johannesen, P. A., Lyras, D., et al. (2017). Conjugation-mediated horizontal gene transfer of *Clostridium perfringens* plasmids in the chicken gastrointestinal tract results in the formation of new virulent strains. *Appl. Environ. Microbiol.* doi:10.1128/AEM.01814-17.

Lamas, A., Miranda, J. M., Regal, P., Vázquez, B., Franco, C. M., and Cepeda, A. (2018). A comprehensive review of non-enterica subspecies of *Salmonella enterica*. *Microbiol. Res.* 206, 60–73. doi:10.1016/j.micres.2017.09.010.

Lan, P. T. N., Hayashi, H., Sakamoto, M., and Benno, Y. (2002). Phylogenetic Analysis of Cecal Microbiota in Chicken by the Use of 16S rDNA Clone Libraries. *Microbiol. Immunol.* 46, 371–382.

Landers, T. F., Cohen, B., Wittum, T. E., and Larson, E. L. (2012). A Review of Antibiotic Use in Food Animals: Perspective, Policy, and Potential.

Landoni, M. F., and Albarellos, G. (2015). The use of antimicrobial agents in broiler chickens. *Vet. J.* 205, 21–7. doi:10.1016/j.tvjl.2015.04.016.

Larsen, N., Nissen, P., and Willats, W. G. T. (2007). The effect of calcium ions on adhesion and
competitive exclusion of *Lactobacillus* ssp. and *E. coli* O138. *Int. J. Food Microbiol.* 114, 113-119. doi:10.1016/j.ijfoodmicro.2006.10.033.

Laukens, D., Brinkman, B. M., Raes, J., De Vos, M., and Vandenabeele, P. (2015). Heterogeneity of the gut microbiome in mice: Guidelines for optimizing experimental design. *FEMS Microbiol. Rev.* 40, 117-132. doi:10.1093/femsre/fuv036.

Laxminarayan, R., Van Boeckel, T., and Teillant, A. (2015). The economic costs of withdrawing antimicrobial growth promoters from the livestock sector. *OECD Food, Agric. Fish. Pap.* doi:http://dx.doi.org/10.1787/5js64kst5wvl-en.

Lebeer, S., Vanderleyden, J., and Keersmaecker, S. C. J. De (2008). Genes and molecules of lactobacilli supporting probiotic action. *Microbiol. Mol. Biol. Rev.* 72, 728-764. doi:10.1128/MMBR.00017-08.

Leccese Terraf, M. C., Juárez Tomás, M. S., Nader-Macías, M. E. F., and Silva, C. (2012). Screening of biofilm formation by beneficial vaginal lactobacilli and influence of culture media components. *J. Appl. Microbiol.* 113, 1517-1529. doi:10.1111/j.1365-2672.2012.05429.x.

Lee, C. W., and Saif, Y. M. (2009). Avian influenza virus. *Comp. Immunol. Microbiol. Infect. Dis.* 32, 301-310. doi:10.1016/j.cimid.2008.01.007.

Lee, J. su, Chung, M.-J., and Seo, J.-G. (2013). *In Vitro Evaluation of Antimicrobial Activity of Lactic Acid Bacteria against Clostridium difficile*. doi:10.5487/TR.2013.29.2.099.

Lee, K. W., Lillehoj, H. S., Jeong, W., Jeoung, H. Y., and An, D. J. (2018). Avian necrotic enteritis : Experimental models, host immunity, pathogenesis, risk factors, and vaccine development. *Poult. Sci.* 90, 1381-1390. doi:10.3382/ps.2010-01319.

Lepp, D., Roxas, B., Parreira, V. R., Marri, P. R., Rosey, E. L., Gong, J., et al. (2010). Identification of Novel Pathogenicity Loci in *Clostridium perfringens* Strains That Cause Avian Necrotic Enteritis. *PLoS One* 5, e10795. doi:10.1371/journal.pone.0010795.

Levy, S. B. (1992). *The antibiotic paradox: how miracle drugs are destroying the miracle*. New York: Plenum.

Lewis, K. (2013). Platforms for antibiotic discovery. *Nat. Rev. Drug Discov.* 12, 371-387. doi:10.1038/nrd3975.

Li, Q., Liu, X., and Zhou, J. (2015). Aggregation and adhesion abilities of 18 lactic acid bacteria strains isolated from traditional fermented food. *Int. J. Agric. Policy Res.* 3, 84-92. doi:10.15739/IJAPR.030.

Li, Z., Wang, W., Liu, D., and Guo, Y. (2018). Effects of *Lactobacillus acidophilus* on the growth performance and intestinal health of broilers challenged with *Clostridium perfringens*. *J. Anim. Sci. Biotechnol.* 9, 1-10.

Li, Z., Wang, W., Lv, Z., Liu, D., Guo, Y., Li, Z., et al. (2017). *Bacillus subtilis* and yeast cell wall improve the intestinal health of broilers challenged by *Clostridium perfringens*. *Br. Poult. Sci.* 58, 635-643. doi:10.1080/00071668.2017.1370697.

Liao, S. F., and Nyachoti, C. M. (2017). Using probiotics to improve swine gut health and nutrient utilization. *Anim. Nutr.* 3, 331-343. doi:10.1016/j.aninu.2017.06.007.

Linares, D. M., Gómez, C., Renes, E., Fresno, J. M., Tornadijo, M. E., Ross, R. P., et al. (2017). Lactic Acid Bacteria and Bifidobacteria with Potential to Design Natural Biofunctional Health-Promoting Dairy Foods. *Front. Microbiol.* 8, 846. doi:10.3389/fmicb.2017.00846.

Lindgren, S. E., and Dobrogosz, W. J. (1990). Antagonistic activities of lactic acid bacteria in food and feed fermentations. *FEMS Microbiol. Lett.* 87, 149-164. doi:10.1016/0378-1097(90)90703-S.
Liu, Y., Li, Y., Shi, T., Zhao, J., Wang, H., Liu, T., et al. (2016). The optimization of spray drying process of *Lactobacillus reuteri*. *LWT - Food Sci. Technol.* 68, 615-618. doi:10.1016/j.lwt.2016.01.008.

Ljungh, Å., and Wadström, T. (2006). *Lactic Acid Bacteria as Probiotics Further Reading*.

Lu, J., Idris, U., Harmon, B., Maurer, J. J., Lee, M. D., and Hofacre, C. (2003). Diversity and Succession of the Intestinal Bacterial Community of the Maturing Broiler Chicken Diversity and Succession of the Intestinal Bacterial Community of the Maturing Broiler Chicken. *Appl. Environ. Microbiol.* 69, 6816-6824. doi:10.1128/AEM.69.11.6816.

Lund, P., Tramonti, A., and De Biase, D. (2014). Coping with low pH: molecular strategies in neutralophilic bacteria. *FEMS Microbiol. Lett.* 38, 1091-1125. doi:10.1111/1574-6976.12076.

M'Sadeq, S. A., Wu, S., Swick, R. A., and Choct, M. (2015). Towards the control of necrotic enteritis in broiler chickens with in-feed antibiotics phasing-out worldwide. *Anim. Nutr.* 1, 1-11. doi:10.1016/j.aninu.2015.02.004.

Mackenzie, D. A., Jeffers, F., Parker, M. L., Vibert-vallet, A., Bongaerts, R. J., Roos, S., et al. (2010). Strain-specific diversity of mucus-binding proteins in the adhesion and aggregation properties of *Lactobacillus reuteri*. *Microbiology* 156, 3368-3378. doi:10.1099/mic.0.043265-0.

Macwana, S. J., and Muriana, P. M. (2012). A “bacteriocin PCR array” for identification of bacteriocin-related structural genes in lactic acid bacteria. *J. Microbiol. Methods* 88, 197-204. doi:10.1016/j.mimet.2011.11.008.

Madsen, K. (2006). Probiotics and the Immune Response. *J. Clin Gastroenterol* 40, 232-234.

Madsen, K. L. (2012). Enhancement of epithelial barrier function by probiotics. *J. Epithel. Biol. Pharmacol.* 5, 55-59.

Mainville, I., Arcand, Y., and Farnworth, E. R. (2005). A dynamic model that simulates the human upper gastrointestinal tract for the study of probiotics. *Int. J. Food Microbiol.* 99, 287-296. doi:10.1016/j.ijfoodmicro.2004.08.020.

Majeed, H., Lampert, A., Ghazaryan, L., and Gillor, O. (2013). The Weak Shall Inherit: Bacteriocin-Mediated Interactions in Bacterial Populations. *PLoS One* 8. doi:10.1371/journal.pone.0063837.

Mappley, L. J., Tchorzewska, M. A., Cooley, W. A., Woodward, M. J., and La Ragione, R. M. (2011). Lactobacilli Antagonize the Growth, Motility, and Adherence of *Brachyspira pilosicoli*: a Potential Intervention against Avian Intestinal Spirochetosis ☐. *Appl. Environ. Microbiol.* 77, 5402-5411. doi:10.1128/AEM.00185-11.

Maron, D. F., Smith, T. J. S., and Nachman, K. E. (2013). Restrictions on antimicrobial use in food animal production: an international regulatory and economic survey. *Global. Health* 9, 48. doi:10.1186/1744-8603-9-48.

Marrec, C. L. E., Hyronimus, B., Bressollier, P., Verneuil, B., and Urdaci, M. C. (2000). Biochemical and Genetic Characterization of Coagulin, a New Antilisterial Bacteriocin in the Pediocin Family of Bacteriocins, Produced by *Bacillus coagulans* I 4. *Appl. Environ. Microbiol.* 66, 5213-5220.

Marshall, B. M., and Levy, S. B. (2011). Food animals and antimicrobials: Impacts on human health. *Clin. Microbiol. Rev.* 24, 718-733. doi:10.1128/CMR.00002-11.

Martin, F.-P. J., Wang, Y., Sprenger, N., Yap, I., Lundstedt, T., Lek, P., et al. (2008). Probiotic modulation of symbiotic gut microbial – host metabolic interactions in a humanized microbiome mouse model. *Mol. Syst. Biol.* 4, 157. doi:10.1038/msb4100190.
Martinez-Haro, M., Taggart, M. A., Green, A. J., and Mateo, R. (2009). Avian Digestive Tract Simulation To Study the Effect of Grit Geochemistry and Food on Ph Shot Eioaccessihility. *Environmetnal Sci. Technol.* 43, 3-9.

Martínez Cruz, P., Ibáñez, A. L., Monroy Hermosillo, O. A., and Ramírez Saad, H. C. (2012). Use of probiotics in aquaculture. *ISRN Microbiol.* 2012, 1-13. doi:10.5402/2012/916845.

Martoni, C. J., Labb, A., Ganopolsky, J. G., Prakash, S., and Jones, M. L. (2015). Changes in bile acids, FGF-19 and sterol absorption in response to bile salt hydrolase active L. reuteri NCIMB 30242. *Gut Microbes* 6, 57-65.

Mater, D. D. G., Langella, P., Corthier, G., and Flores, M. J. (2007). A probiotic *Lactobacillus* strain can acquire vancomycin resistance during digestive transit in mice. *J. Mol. Microbiol. Biotechnol.* 14, 123-127. doi:10.1159/000106091.

Mathias, A., Duc, M., Favre, L., Benyacoub, J., Blum, S., and Corthesy, B. (2010). Potentiation of polarized intestinal Caco-2 cell responsiveness to probiotics complexed with secretory IgA. *J. Biol. Chem.* 285, 33906-33913. doi:10.1074/jbc.M110.135111.

McReynolds, J. L., Byrd, J. A., Anderson, R. C., Moore, R. W., Edrington, T. S., Genovese, K. J., et al. (2004). Evaluation of immunosuppressants and dietary mechanisms in an experimental disease model for necrotic enteritis. *Poult. Sci.* 83, 1948-1952.

Mekonnen, M. M., and Hoekstra, A. Y. (2012). A Global Assessment of the Water Footprint of Farm Animal Products. *Ecosystems* 15, 401-415. doi:10.1007/s10021-011-9517-8.

Messaoudi, S., Kergourlay, G., Rossero, A., Ferchichi, M., Prévost, H., Drider, D., et al. (2011). Identification of lactobacilli residing in chicken ceca with antagonism against *Campylobacter*. *Int. Microbiol.* 14, 103-110. doi:10.2436/20.1501.01.140.

Messaoudi, S., Madi, A., Prévost, H., Feuilloley, M., Manai, M., Dousset, X., et al. (2012). *In vitro* evaluation of the probiotic potential of *Lactobacillus salivarius* SMXD51. *Anaerobe* 18, 584-589. doi:10.1016/j.anaerobe.2012.10.004.

Metschnikoff, E. (1907). *The prolongation of life. Optimistic studies*. London, UK.

Miljkovic, M., Strahinic, I., Tolinacki, M., Zivkovic, M., and Kojic, S. (2015). AggLb is the largest cell-aggregation factor from *Lactobacillus paracasei* Subsp. *paracasei* BGNJ1-64, functions in collagen adhesion, and pathogen exclusion in vitro. *PLoS One* 10, e0126387. doi:10.1371/journal.pone.0126387.

Millet, S., and Maertens, L. (2011). The European ban on antibiotic growth promoters in animal feed: From challenges to opportunities. *Vet. J.* 187, 143-144. doi:10.1016/j.tvjl.2010.05.001.

Minelli, E. B., and Benini, A. (2008). Relationship between number of bacteria and their probiotic effects. *Microb. Ecol. Health Dis.* 20, 180-183. doi:10.1080/08910600802408095.

Ming, L. C., Rahim, R. A., Wan, H. Y., and Ariff, A. B. (2009). Formulation of protective agents for improvement of *Lactobacillus salivarius* I 24 survival rate subjected to freeze drying for production of live cells in powderized form. *Food Bioprocess Technol.* 2, 431-436. doi:10.1007/s11947-009-0184-0.

Moore, R. J. (2016). Necrotic enteritis predisposing factors in broiler chickens. *Avian Pathol.* 45, 275-281. doi:10.1080/03079457.2016.1150587.

Morar, M., and Wright, G. D. (2010). The Genomic Enzymology of Antibiotic Resistance. *Annu. Rev. Genet.* 44, 25-51. doi:10.1146/annurev-genet-102209-163517.

Moslehi-jenabian, S., Pedersen, L. L., and Jespersen, L. (2010). Beneficial Effects of Probiotic and Food Borne Yeasts on Human Health. *Nutrients* 2, 449-473. doi:10.3390/nu2040449.

Motevaseli, E., Shirzad, M., Akrami, S. M., Mousavi, A. S., Mirsalehian, A., and Modarressi, M. H. (2013). Normal and Tumour cervical cells respond differently to vaginal lactobacilli,
independent of pH and lactate. *J. Med. Microbiol.* 62, 1065-1072.
doi:10.1099/jmm.0.057521-0.

Mottet, A., and Tempio, G. (2017). Reviews Global poultry production : current state and future outlook and challenges. *Worlds. Poult. Sci. J.* 73, 1-12. doi:10.1017/S0043933917000071.

Mountzouris, K. C., Tsitrsikos, P., Palamidi, I., Arvaniti, A., Mohnl, M., Schatzmayr, G., et al. (2010). Effects of probiotic inclusion levels in broiler nutrition on growth performance, nutrient digestibility, plasma immunoglobulins, and cecal microflora composition. *Poult. Sci.* 89, 58-67. doi:10.3382/ps.2009-00308.

Mu, Q., Tavella, V. J., and Luo, X. M. (2018). Role of *Lactobacillus reuteri* in human health and diseases. *Front. Microbiol.* 9, 757. doi:10.3389/fmicb.2018.00757.

Munita, J. M., and Arias, C. A. (2016). Mechanisms of Antibiotic Resistance. *Microbiol. Spectr.* 4, 1-37. doi:10.1128/microbiolspec.VMBF-0016-2015.Mechanisms.

Murphy, D., Ricci, A., Auce, Z., Beechinor, J. G., Bergendahl, H., Da, D., 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, 4666. doi:10.2903/j.efsa.2017.4666.

Murry, A. C., Hinton, A., and Morrison, H. (2004). Inhibition of growth of *Escherichia coli*, *Salmonella* typhimurium, and *Clostridia perfringens* on chicken feed media by *Lactobacillus salivarius* and *Lactobacillus plantarum*. *Int. J. Poult. Sci.* 3, 603-607.

Musikasang, H., Tani, A., H-kittikun, A., and Maneerat, S. (2009). Probiotic potential of lactic acid bacteria isolated from chicken gastrointestinal digestive tract. *World J. Microbiol. Biotechnol.* 25, 1337-1345. doi:10.1007/s11274-009-0020-8.

Nakphaichit, M., Thanomwongwattana, S., Phraephaisarn, C., Sakamoto, N., Keawsompong, S., Nakayama, J., et al. (2011). The effect of including *Lactobacillus reuteri* KUB-AC5 during post-hatch feeding on the growth and ileum microbiota of broiler chickens. *Poult. Sci.* 90, 2753-2765. doi:10.3382/ps.2011-01637.

Nancib, A., Nancib, N., Boubendir, A., and Boudrant, J. (2015). The use of date waste for lactic acid production by a fed-batch culture using *Lactobacillus casei* subsp. *rhamnosus*. *Brazilian J. Microbiol.* 46, 893-902. doi:10.1590/S1517-838246320131067.

Navarro, M., McClane, B., and Uzal, F. (2018). Mechanisms of Action and Cell Death Associated with *Clostridium perfringens* Toxins. *Toxins (Basel)*. 10, 212. doi:10.3390/toxins10050212.

Nayak, S. K. (2011). “Biology of Eukaryotic Probiotics,” in *Probiotics, Microbiology Monographs* 21, ed. M.-T. Liong (Springer-Verlag Berlin Heidelberg), 29–56. doi:10.1007/978-3-642-20838-6.

O'Neill, J. (2014). Antimicrobial Resistance: Tackling a crisis for the health and wealth of nations.

O'Toole, G. O., Kaplan, H. B., and Kolter, R. (2000). Biofilm Formation As Microbial Development. *Annu. Rev. Microbiol.* 54, 49-79. doi:10.1146/annurev.micro.54.1.49.

O'Toole, P. W., and Cooney, J. C. (2008). Probiotic Bacteria Influence the Composition and Function of the Intestinal Microbiota. *Interdiscip. Perspect. Infect. Dis.* doi:10.1155/2008/175285.

Oakley, B. B., Lillehoj, H. S., Kogut, M. H., Kim, W. K., Maurer, J. J., Lee, M. D., et al. (2014). The chicken gastrointestinal microbiome. *FEMS Microbiol. Lett.* 368, 100-112. doi:10.1111/1574-6968.12608.

OECD/FAO (2017). *OECD-FAO Agricultural Outlook* 2017-2026.
doi:http://dx.doi.org/10.1787/agr_outlook-2017-en.

OECD/FAO (2018a). “Meat,” in *OECD/FAO Agricultural Outlook 2018-2027* (OECD Publishing,
Paris/Food and Agriculture Organization of United Nations, Rome), 149-162.
doi:https://doi.org/10.1787/19991142.

OECD/FAO (2018b). OECD - FAO Agricultural Outlook 2018 - 2027. OECD Publishing,
Paris/Food and Agriculture Organization of the United Nations, Rome.
doi:https://doi.org/10.1787/agr_outlook-2018-en.

Oelschlaeger, T. A. (2010). Mechanisms of probiotic actions – A review. *Int. Jl Med. Microbiol.* 300, 57–62. doi:10.1016/j.ijmm.2009.08.005.

Ohland, C. L., and Macnaughton, W. K. (2010). Probiotic bacteria and intestinal epithelial barrier function. *Am. J. Physiol. Liver Physiol.* 298, G807–G819. doi:10.1152/ajpgi.00243.2009.

Ohtani, K., and Shimizu, T. (2015). Regulation of toxin gene expression in *Clostridium perfringens*. *Res. Microbiol.* 166, 280–289. doi:10.1016/j.resmic.2014.09.010.

OIE (2013). Report Of The Meeting Of The Oie Scientific Commission For Animal Diseases.

OIE (2014). Chapter 2.3.6. Avian Tuberculosis. doi:10.15713/ins.mmj.3.

OIE (2018). Code sanitaire pour les animaux terrestres.

Oliveira, B. C. M., and Widmer, G. (2018). Probiotic Product Enhances Susceptibility of Mice to Cryptosporidiosis. *Appl. Environ. Microbiol.* 84. Available at: http://aem.asm.org/content/84/21/e01408-18 abstract.

OMS (2004). Joint FAO/OIE/WHO Expert Workshop on Non-Human Antimicrobial Usage and Antimicrobial Resistance: scientific assessment. Geneva, December 1-5 Available at: http://www.who.int/iris/handle/10665/68883.

Opengart, K. (2008). *Diseases of Poultry. Necrotic enteritis*. 12th ed., ed. and D. E. S. Y. M. Saif, A. M. Fadly, J. R. Glisson, L. McDougald, L. K. Nolan ed. Wiley-Blackwell Publishing, Ames, IA.

Orozco, F. G., and Zuluaga, F. (2014). Lactic Acid Yield Using Different Bacterial Strains, Its Purification, and Polymerization through Ring-Opening Reactions. *Int. J. Polym. Sci.* Article ID.

Ouwehand, A. C. (2017). A review of dose-responses of probiotics in human studies. *Benef. Microbes* 8, 143-151. doi:10.3920/BM2016.0140.

Ouwehand, A. C., and Salminen, S. (2003). *In vitro* Adhesion Assays for Probiotics and their *in vivo* Relevance: A Review. *Microb. Ecol. Health Dis.* 15, 175-184. doi:10.1080/08910600310019886.

Ozen, M., and Dinleyici, E. C. (2015). The history of probiotics : the untold story. *Benef. Microbes* 6, 159-165. doi:10.3920/BM2014.0103.

Page, S. W., and Gautier, P. (2012). Use of antimicrobial agents in livestock. *Rev. sci. tech. Off. int. Epiz.* 31, 145-188. doi:10.20506/rst.31.1.2106.

Paiva, D. M., Walk, C. L., and McElroy, A. P. (2013). Influence of dietary calcium level, calcium source, and phytase on bird performance and mineral digestibility during a natural necrotic enteritis episode. *Poult. Sci.* 92, 3125-3133.

Paiva, D., and McElroy, A. (2014). Necrotic enteritis: Applications for the poultry industry. *J. Appl. Poult. Res.* 23, 557-566. doi:10.3382/japr.2013-00925.

Palliyeguru, M. W. C. D., and Rose, S. P. (2014). Sub-clinical necrotic enteritis: its aetiology and predisposing factors in commercial broiler production. *Worlds. Poult. Sci. J.* 70, 803–816. doi:10.1017/S0043933914000865.

Papadimitriou, K., Zoumpopoulou, G., Foligné, B., Alexandraki, V., Kazou, M., Pot, B., et al. (2015). Discovering probiotic microorganisms: *in vitro*, *in vivo*, genetic and omics approaches. *Front. Microbiol.* 6, 58. doi:10.3389/fmicb.2015.00058.
Park, C., and Seo, Y. (2015). Heat Shock Proteins: A Review of the Molecular Chaperones for Plant Immunity. *Plant Pathol. J.* 31, 323–333.

Park, S. S., Lillehoj, H. S., Allen, P. C., Park, D. W., Fitzcoy, S., Daniel, A., et al. (2008). Immunopathology and cytokine responses in broiler chickens coinfected with *Eimeria maxima* and *Clostridium perfringens* with the use of an animal model of necrotic enteritis. *Avian Dis.* 52, 14–22.

Park, Y. H., Hamidon, F., Rajangan, C., Soh, K. P., Gan, C. Y., Lim, T. S., et al. (2016). Application of probiotics for the production of safe and high-quality poultry meat. *Korean J. Food Sci. Anim. Resour.* 36, 567–576. doi:10.5851/kosfa.2016.36.5.567.

Parreira, V. R., Costa, M., Eikmeyer, F., Blom, J., and Prescott, J. F. (2012). Sequence of Two Plasmids from *Clostridium perfringens* Chicken Necrotic Enteritis Isolates and Comparison with *C. perfringens* Conjugative Plasmids. *PLoS One* 7, e49753. doi:10.1371/journal.pone.0049753.

Patel, S., and Goyal, A. (2012). The current trends and future perspectives of prebiotics research: a review. *3 Biotech* 2, 115–125. doi:10.1007/s13205-012-0044-x.

Pathak, S., Awuh, J. A., Leversen, N. A., Flo, T. H., and Åsjø, B. (2012). Counting mycobacteria in infected human cells and mouse tissue: A comparison between qPCR and CFU. *PLoS One* 7. doi:10.1371/journal.pone.0034931.

Patz, J. A., and Hahn, M. B. (2013). *One Health: The Human-Animal-Environment Interfaces in Emerging Infectious Diseases*., eds. J. S. Mackenzie, M. Jeggo, P. Daszak, and J. A. Richt Berlin, Heidelberg: Springer Berlin Heidelberg doi:10.1007/978-3-642-36889-9.

Pavel, A. B., and Vasile, C. I. (2012). PyElph - a software tool for gel images analysis and phylogenetics. *BMC Bioinformatics* 13. doi:10.1186/1471-2105/13/9.

Peng, Q., Zeng, X. F., Zhu, J. L., Wang, S., Liu, X. T., Hou, C. L., et al. (2016). Effects of dietary *Lactobacillus plantarum* B1 on growth performance, intestinal microbiota, and short chain fatty acid profiles in broiler chickens. *Poult. Sci.* 95, 893–900. doi:doi.org/10.3382/ps/pev435.

Perdigon, G., Alvarez, S., Rachid, M., Agüero, G., and Gobbato, N. (1995). Immune System Stimulation by Probiotics. *J. Dairy Sci.* 78, 1597–1606. doi:10.3168/jds.S0022-0302(95)76784-4.

Pérez Ibarreche, M., Castellano, P., and Vignolo, G. (2014). Evaluation of anti-*Listeria* meat borne *Lactobacillus* for biofilm formation on selected abiotic surfaces. *Meat Sci.* 96, 295–303. doi:10.1016/j.meatsci.2013.07.010.

Pessione, E. (2012). Lactic acid bacteria contribution to gut microbiota complexity: lights and shadows. *Front. Cell. Infect. Microbiol.* 2, 86. doi:10.3389/fcimb.2012.00086.

Pisano, M. B., Viale, S., Conti, S., Fadda, M. E., Deplano, M., Melis, M. P., et al. (2014). Preliminary Evaluation of Probiotic Properties of *Lactobacillus* Strains Isolated from Sardinian Dairy Products. *Biomed Res. Int.* Article ID, 9 pages. doi:10.1155/2014/286390.

Polak-Berecka, M., Wasko, A., Paduch, R., Skrzypek, T., and Sroka-Bartnicka, A. (2014). The effect of cell surface components on adhesion ability of *Lactobacillus rhamnosus*. *Antonie van Leewenhoek* 106, 751–762. doi:10.1007/s10482-014-0245-x.

Poolman, B., and Konings, W. N. (1993). Secondary solute transport in bacteria. *Biochim. Biophys. Acta* 1183, 5–39. doi:10.1016/0005-2728(93)90003-X.

Porter, R. E. (1998). Bacterial enteritides of poultry. *Poult. Sci.* 77, 1159–1165. doi:10.1093/ps/77.8.1159.

Pourabedin, M., Guan, L., and Zhao, X. (2015). Xylo-oligosaccharides and virginiamycin differentially modulate gut microbial composition in chickens. *Microbiome* 3, 1–12.
doi:10.1186/s40168-015-0079-4.

Prescott, J. F., Parreira, V. R., Gohari, I. M., Lepp, D., and Gong, J. (2016). The pathogenesis of necrotic enteritis in chickens: what we know and what we need to know: a review. *Avian Pathol.* 45, 288-294. doi:10.1080/03079457.2016.1139688.

Prescott, J. F., Sivendra, R., and Barnum, D. A. (1978). The use of bacitracin in the prevention and treatment of experimentally-induced Necrotic Enteritis in the chicken. *Can. Vet. J.* 19, 181-183.

Qing, X., Zeng, D., Wang, H., Ni, X., Liu, L., Lai, J., et al. (2017). Preventing subclinical necrotic enteritis through *Lactobacillus johnsonii* BS15 by ameliorating lipid metabolism and intestinal microflora in broiler chickens. *AMB Express* 7, 139. doi:10.1186/s13568-017-0439-5.

Quinteiro-Filho, W. M., Brisbin, J. T., Hodgins, D. C., and Sharif, S. (2015). *Lactobacillus* and *Lactobacillus* cell-free culture supernatants modulate chicken macrophage activities. *Res. Vet. Sci.* 103, 170-175. doi:10.1016/j.rvsc.2015.10.005.

Quinto, E. J., Jiménez, P., Caro, I., Tejero, J., and Mateo, J. (2014). Probiotic lactic acid bacteria: A review. *Food Nutr. Sci.* 5, 1765-1775.

Rabin, N., Zheng, Y., Du, Y., Bonsu, E., and Sintim, H. O. (2015). Agents that inhibit bacterial biofilm formation. *Future Med. Chem.* 7, 647-671.

Raftis, E. J., Salvetti, E., Torriani, S., Felis, G. E., and Toole, P. W. O. (2011). Genomic Diversity of *Lactobacillus salivarius*. *Appl. Environ. Microbiol.* 77, 954-965. doi:10.1128/AEM.01687-10.

Rao, R. K., and Samak, G. (2013). Protection and Restitution of Gut Barrier by Probiotics: Nutritional and Clinical Implications. *Curr. Nutr. Food Sci.* 9, 99-107.

Rappé, M. S., and Giovannoni, S. J. (2003). The Uncultured Microbial Majority. *Annu. Rev. Microbiol.* 57, 369-394. doi:10.1146/annurev.micro.57.030502.090759.

Rasch, M. (2002). The influence of temperature, salt and pH on the inhibitory effect of reuterin on *Escherichia coli*. *Int. J. Food Microbiol.* 72, 225-231. doi:10.1016/S0168-1605(01)00637-7.

Ratsep, M., Naaber, P., Kõljalg, S., Smidt, I., Shkut, E., and Sepp, E. (2014). Effect of *Lactobacillus plantarum* Strains on Clinical Isolates of *Clostridium difficile* in vitro. *J. Probiotics Health.* 2. doi:10.4172/2329-8901.1000119.

Rees, J. H., Soudain, S. E., Gregson, N. A., and Hughes, R. A. C. (1995). *Campylobacter jejuni* Infection and Guillain-Barré Syndrome. *N. Engl. J. Med.* 333, 1374-1379. doi:10.1056/NEJM19951123332102.

Reis, J. A., Paula, A. T., Casarotti, S., and Penna, A. L. B. (2012). Lactic Acid Bacteria Antimicrobial Compounds: Characteristics and Applications. *Food Eng. Rev.* 4, 124-140. doi:10.1007/s12393-012-9051-2.

Riddell, C., and Kong, X. (1992). The Influence of Diet on Necrotic Enteritis in Broiler Chickens. *Avian Dis.* 36, 499-503.

Riley, M. (2009). Bacteriocins, Biology, Ecology, and Evolution. *Encycl. Microbiol.*, 4600.

Rinttilä, T., and Apajalahti, J. (2013). Intestinal microbiota and metabolites — Implications for broiler chicken health and performance 1. *J. Appl. Poult. Res.* 22, 647-658.

Risøen, P. A., Brurberg, M. B., Eijsink, V. G. H., and Nes, I. F. (2000). Functional analysis of promoters involved in *quorum sensing*-based regulation of bacteriocin production in *Lactobacillus*. *Mol. Microbiol.* 37, 619-628. doi:10.1046/j.1365-2958.2000.02029.x.

Rodrigues, I., Svihus, B., Bedford, M. R., Gous, R., and Choct, M. (2018). Intermittent lighting improves resilience of broilers during the peak phase of sub-clinical necrotic enteritis
infection. *Poult. Sci.* 97, 438-446. doi:10.3382/ps/pex315.

Rood, J. I., Adams, V., Lacey, J., Lyras, D., Mcclane, B. A., Melville, S. B., et al. (2018). Anaerobe Expansion of the *Clostridium perfringens* toxin-based typing scheme. *Anaerobe*, 1-6. doi:10.1016/j.anaerobe.2018.04.011.

Rood, J. I., Keyburn, A. L., and Moore, R. J. (2016). NetB and necrotic enteritis : the hole movable story. *Avian Pathol.* 45, 295-301. doi:10.1080/03079457.2016.1158781.

Roos, S., Lindgren, S., and Jonsson, H. (1999). Autoaggregation of *Lactobacillus reuteri* is mediated by a putative DEAD-box helicase. *Mol. Microbiol.* 32, 427-436.

Rossolini, G. M. (2015). Multidrug-resistant and extremely drug-resistant bacteria: are we facing the end of the antibiotic era? *J. Siena Acad. Sci.* 7. doi:10.4081/jsas.2015.6409.

Rossolini, G. M., Arena, F., Pecile, P., and Pollini, S. (2014). Update on the antibiotic resistance crisis. *Curr. Opin. Pharmacol.* 18, 56-60. doi:10.1016/j.coph.2014.09.006.

Roto, S. M., Kwon, Y. M., and Rick, S. C. (2016). Applications in ovo technique for the optimal development of the gastrointestinal tract and the potential influence on the establishment of its microbiome in poultry. *Front. Vet. Sci.* 3, 63. doi:10.3389/fvets.2016.00063.

Roy, P., Dhillon, A. S., Shivaprasad, H. L., Schaberg, D. M., Bandli, D., and Johnson, S. (2001). Pathogenicity of different serogroups of avian salmonellae in specific-pathogen-free chickens. *Avian Dis.* 45, 922-937. doi:10.2307/1592871.

Ruiz, L., Margolles, A., and Sánchez, B. (2013). Bile resistance mechanisms in *Lactobacillus* and Bifidobacterium. *Front. Microbiol.* 4, 1-8. doi:10.3389/fmicb.2013.00396.

Russo, P., Capozzi, V., Arena, M. P., Spadaccino, G., Dueñas, M. T., López, P., et al. (2014). Riboflavin-overproducing strains of *Lactobacillus fermentum* for riboflavin-enriched bread. *Appl Microbiol Biotechnol* 98, 3691-3700. doi:10.1007/s00253-013-5484-7.

Sadeyen, J.-R., Trotereau, J., Protais, J., Beaumont, C., Sellier, N., Salvat, G., et al. (2006). *Salmonella* carrier-state in hens : study of host resistance by a gene expression approach. 8, 1308-1314. doi:10.1016/j.micinf.2005.12.014.

Sakurai, J., Nagahama, M., and Oda, M. (2004). Clostridium perfringens alpha-Toxin : Characterization and mode of action. *J. Biochem.* 136, 569-574. doi:10.1093/jb/mvh161.

Salas-Jara, M., Ilabaca, A., Vega, M., and García, A. (2016). Biofilm Forming *Lactobacillus*: New Challenges for the Development of Probiotics. *Microorganisms* 4, 35. doi:10.3390/microorganisms4030035.

Salminen, M. K., Rautelin, H., Tynkkynen, S., Poussa, T., Saxelin, M., Valtonen, V., et al. (2004). *Lactobacillus* Bacteremia, Clinical Significance, and Patient Outcome, with Special Focus on Probiotic L. rhamnosus GG. *Clin. Infect. Dis.* 38, 62-9.

Salvetti, E., Torriani, S., and Felis, G. E. (2012). The Genus *Lactobacillus*: A Taxonomic Update. *Probiotics Antimicrob. Proteins* 4, 217-226. doi:10.1007/s12602-012-9117-8.

Sambuy, Y., De Angelis, I., Ranaldi, G., Scarino, M. L., Stammati, A., and Zucco, F. (2005). The Caco-2 cell line as a model of the intestinal barrier: influence of cell and culture-related factors on Caco-2 cell functional characteristics. *Cell Biol. Toxicol.* 21, 1-26. doi:10.1007/s10565-005-0085-6.

Sanders, P., Perrin-Guyomard, A., and Moulin, G. (2017). Évolution de l' utilisation des antibiotiques en production animale. *Cah. Nutr. diétetique* 52, 301-311. doi:10.1016/j.cnd.2017.06.002.

Santos, R. L., Raffatellu, M., Bevins, C. L., Adams, L. G., Tsolis, M., and Ba, A. J. (2009). Life in the inflamed intestine, *Salmonella* style. *Trends Microbiol.* 17, 498-506. doi:10.1016/j.tim.2009.08.008.
Sarangi, N. R., Babu, L. K., Kumar, A., Pradhan, C. R., Pati, P. K., and Mishra, J. P. (2016). *Probiotics in Animal Nutrition*. doi:10.14202/vetworld.2016.313-319.

Sato, Y., Wigle, W. L., Gallagher, S., Johnson, A. L., Sweeney, R. W., and Wakenell, P. S. (2016). Outbreak of Type C Botulism in Commercial Layer Chickens. *Avian Dis.* 60, 90–94. doi:10.1637/11293-100415-Case.1.

Savva, C. G., Da Costa, S. P. F., Bokori-Brown, M., Naylor, C. E., Cole, A. R., Moss, D. S., et al. (2013). Molecular architecture and functional analysis of NetB, a pore-forming toxin from *Clostridium perfringens*. *J. Biol. Chem.* 288, 3512–3522. doi:10.1074/jbc.M112.430223.

Schaefer, L., Auchtung, T. A., Hermans, K. E., Whitehead, D., Borhan, B., and Britton, R. A. (2010). The antimicrobial compound reuterin (3-hydroxypropionaldehyde) induces oxidative stress via interaction with thiol groups. *Microbiology* 156, 1589–1599. doi:10.1099/mic.0.035642-0.

Schatzmayr, G., and Streit, E. (2013). Global occurrence of mycotoxins in the food and feed chain: facts and figures. *World Mycotoxin J.* 6, 213–222. doi:10.3920/WMJ2013.1572.

Schillinger, U., and Lücke, F. K. (1989). Antibacterial activity of *Lactobacillus sake* isolated from meat. *Appl. Environ. Microbiol.* 55, 1901–1906. doi:10.1016/S0168-1605(03)00051-5.

Schnürer, J., and Magnusson, J. (2005). Antifungal lactic acid bacteria as biopreservatives. *Trends Food Sci. Technol.* 16, 70–78. doi:10.1016/j.tifs.2004.02.014.

Seddik, H. A., Bendali, F., Gancel, F., Fliss, I., Spano, G., and Drider, D. (2017). *Lactobacillus plantarum* and Its Probiotic and Food Potentialities. *Probiotics Antimicrob. Proteins* 9, 111–122. doi:10.1007/s12602-017-9264-z.

Seo, J. K., Kim, S. W., Kim, M. H., Upadhaya, S. D., Kam, D. K., and Ha, J. K. (2010). Direct-fed microbials for ruminant animals. *Asian-Australasian J. Anim. Sci.* 23, 1657–1667. doi:10.5713/ajas.2010.r.08.

Servin, A. L., and Coconnier, M.-H. (2003). Adhesion of probiotic strains to the intestinal mucosa and interaction with pathogens. *Best Pract. Res. Clin. Gastroenterol.* 17, 741–754. doi:10.1016/S1521-6918(03)00052-0.

Sha, Y., Wang, B., Liu, M., Jiang, K., and Wang, L. (2016a). Interaction between *Lactobacillus pentosus* HC-2 and *Vibrio parahaemolyticus* E1 in *Litopenaeus vannamei* in vivo and in vitro. *Aquaculture* 465, 117–123. doi:10.1016/j.aquaculture.2016.09.007.

Sha, Y., Wang, L., Liu, M., Jiang, K., Xin, F., and Wang, B. (2016b). Effects of lactic acid bacteria and the corresponding supernatant on the survival, growth performance, immune response and disease resistance of *Litopenaeus vannamei*. *Aquaculture* 452, 28–36. doi:10.1016/j.aquaculture.2015.10.014.

Sharifuzzaman, S. M., and Austin, B. (2017). “Probiotics for Disease Control in Aquaculture,” in *Diagnosis and Control of Diseases of Fish and Shellfish*, eds. B. Austin and A. Newaj-Fyzul (John Wiley & Sons Ltd), 189–222. doi:10.1002/9781119152125.ch8.

Shekh, S. L., Dave, J. M., and Vyas, B. R. M. (2016). Characterization of *Lactobacillus plantarum* strains for functionality, safety and γ-amino butyric acid production. *LWT - Food Sci. Technol.* 74, 234–241. doi:10.1016/j.lwt.2016.07.052.

Shen, S., Samaranayake, L. P., and Yip, H. K. (2005). Coaggregation profiles of the microflora from root surface caries lesions. *Arch. Oral Biol.* 50, 23–32. doi:10.1016/j.archoralbio.2004.07.002.

Shida, K., and Nanno, M. (2008). Probiotics and immunology: separating the wheat from the chaff. *Trends Immunol.* 29, 565–573. doi:10.1016/j.it.2008.07.011.

Shimizu, T., Ohtani, K., Hirakawa, H., Ohshima, K., Yamashita, A., and Shiba, T. (2002).
Complete genome sequence of *Clostridium perfringens*, an anaerobic flesh-eater. *PNAS* 99, 996–1001.

Shojadoost, B., Peighambari, S. M., and Nikpiran, H. (2013). Effects of virginiamycin against experimentally induced necrotic enteritis in broiler chickens vaccinated or not with an attenuated coccidial vaccine. *J. Appl. Poult. Res.* 22, 160–167.

Shojadoost, B., Vince, A. R., and Prescott, J. F. (2012). The successful experimental induction of necrotic enteritis in chickens by *Clostridium perfringens*: a critical review. *Vet. Res.* 43. doi:10.1186/1297-9716-43-74.

Silva, J., Leite, D., Fernandes, M., Mena, C., Gibbs, P. A., and Teixeira, P. (2011). *Campylobacter* spp. as a foodborne pathogen: a review. *Front. Microbiol.* 2, Article 200. doi:10.3389/fmicb.2011.00200.

Singh, V. P. (2018). Recent approaches in food bio-preservation-a review. *Open Vet. J.* 8, 104–111.

Skarin, H., Tevell Åberg, A., Woudstra, C., Hansen, T., Löfström, C., Koene, M., et al. (2013). The Workshop on Animal Botulism in Europe. *Biosecurity and Bioterrorism*, S183–S190. doi:10.1089/bsp.2012.0076.

Smyth, J. A. (2016). Pathology and diagnosis of necrotic enteritis: is it clear-cut? *Avian Pathol.* 45, 282–287. doi:10.1080/03079457.2016.1158780.

Snyder, L. (2000). HPLC: Past and present. *Anal. Chem.* 72, 412–420. Available at: http://www.scopus.com/inward/record.url?eid=2-s2.0-0034214082&partnerID=40&md5=9cb46335fc98ed115b989850f36cbaa3.

Songer, J. G. (1996). Clostridial enteric diseases of domestic animals. *Clin. Microbiol. Rev.* 9, 216–234.

Souillard, R., Woudstra, C., Le Maréchal, C., Dia, M., Bayon-Auboyer, M. H., Chemaly, M., et al. (2014). Investigation of *Clostridium botulinum* in commercial poultry farms in France between 2011 and 2013. *Avian Pathol.* 43, 458–464. doi:10.1080/03079457.2014.957644.

Stanley, D., Geier, M. S., Chen, H., Hughes, R. J., and Moore, R. J. (2015). Comparison of fecal and cecal microbiotas reveals qualitative similarities but quantitative differences. *BMC Microbiol.* 15, 1–11. doi:10.1186/s12866-015-0388-6.

Stanley, D., Hughes, R. J., and Moore, R. J. (2014). Microbiota of the chicken gastrointestinal tract: Influence on health, productivity and disease. *Appl. Microbiol. Biotechnol.* 98, 4301–4310. doi:10.1007/s00253-014-5646-2.

Stanojević-Nikolić, S., Dimić, G., Mojović, L., Pejin, J., Djukić-Vuković, A., and Kocić-Tanackov, S. (2016). Antimicrobial Activity of Lactic Acid Against Pathogen and Spoilage Microorganisms. *J. Food Process. Preserv.* 40, 990–998. doi:10.1111/jfpp.12679.

Star, L., Rovers, M., Corrent, E., and Klis, J. D. Van Der (2012). Threonine requirement of broiler chickens during subclinical intestinal *Clostridium* infection. *Poult. Sci.* 91, 643–652.

Stein, T. (2005). *Bacillus subtilis* antibiotics: structures, syntheses and specific functions. *Mol. Microbiol.* 56, 845–857. doi:10.1111/j.1365-2958.2005.04587.x.

Stenlid, J., Karlsson, J. O., and Högberg, N. (1994). Intraspecific genetic variation in *Heterobasidion annosum* revealed by amplification of minisatellite DNA. *Mycol. Res.* 98, 57–63. doi:10.1016/S0953-7562(09)80337-7.

Stern, N. J., Eruslanov, B. V., Pokhilenko, V. D., Kovalev, Y. N., Volodina, L. L., Perelygin, V. V., et al. (2008). Bacteriocins reduce *Campylobacter jejuni* colonization while bacteria producing bacteriocins are ineffective. *Microb. Ecol. Health Dis.* 20, 74–79. doi:10.1080/08910600802030196.
Stern, N. J., Svetoch, E. A., Eruslanov, B. V., Perelygin, V. V., Mitsevich, E. V., Mitsevich, I. P., et al. (2006). Isolation of a *Lactobacillus salivarius* strain and purification of its bacteriocin, which is inhibitory to *Campylobacter jejuni* in the chicken gastrointestinal system. *Antimicrob. Agents Chemother.* 50, 3111–3116. doi:10.1128/AAC.00259-06.

Stordeur, P., and Mainil, J. (2002). La colibacillose aviaire. *Ann. Med. Vet.* 146, 11–18.

Sun, Q., Liu, D., and Guo, S. (2015). Effects of dietary essential oil and enzyme supplementation on growth performance and gut health of broilers challenged by *Clostridium perfringens*. *Anim. Feed Sci. Technol.* 207, 234–244. doi:10.1016/j.anifeedsci.2015.06.021.

Surendran Nair, M., Amalaradjou, M. A., and Venkitanarayanan, K. (2017). *Antivirulence Properties of Probiotics in Combating Microbial Pathogenesis*. Elsevier Ltd doi:10.1016/bs.aambs.2016.12.001.

Svanström, Å., Boveri, S., Boström, E., and Melin, P. (2013). The lactic acid bacteria metabolite phenyllactic acid inhibits both radial growth and sporulation of filamentous fungi. *BMC Res. Notes* 6, 464.

Svihus, B. (2014). Function of the digestive system. *J. Appl. Poult. Res.* 23, 306–314. doi:10.3382/japr.2014-00937.

Tachedjian, G., Aldunate, M., Bradshaw, C. S., and Cone, R. A. (2017). The role of lactic acid production by probiotic *Lactobacillus* species in vaginal health. *Res. Microbiol.* 168, 782–792. doi:10.1016/j.resmic.2017.04.001.

Taheri, H. R., Moravej, H., Tabandeh, F., Zaghari, M., and Shivazad, M. (2009). Screening of lactic acid bacteria toward their selection as a source of chicken probiotic. *Poult. Sci.* 88, 1586–1593. doi:10.3382/ps.2009-00041.

Tan, Z., Luo, J., Liu, F., Zhang, Q., and Jia, S. (2015). “Effects of pH, Temperature, Storage Time, and Protective Agents on Nisin Antibacterial Stability,” in *Advances in Applied Biotechnology*, eds. T. Zhang and M. Nakajima, 305–312. doi:10.1007/978-3-662-46318-5.

Tannock, G. W., Ghazally, S., Walter, J., Loach, D., Brooks, H., Cook, G., et al. (2005). Ecological behavior of *Lactobacillus reuteri* 100-23 is affected by mutation of the luxS gene. *Appl. Environ. Microbiol.* 71, 8419–8425. doi:10.1128/AEM.71.12.8419.

Tareb, R., Bernardeau, M., Gueguen, M., and Vernoux, J. P. (2013). *In vitro* characterization of aggregation and adhesion properties of viable and heat-killed forms of two probiotic *Lactobacillus* strains and interaction with foodborne zoonotic bacteria, especially *Campylobacter jejuni*. *J. Med. Microbiol.* 62, 637–649. doi:10.1099/jmm.0.049965-0.

Tellez, G., Pixley, C., Wolfenden, R. E., Layton, S. L., and Hargis, B. M. (2012). Probiotics/direct fed microbials for *Salmonella* control in poultry. *Food Res. Int.* 45, 628–633. doi:10.1016/j.foodres.2011.03.047.

Thachil, A. J., Mccomb, B., Early, M. M., Heeder, C., and Nagaraja, K. V (2012). Clostridium perfringens and *Clostridium septicum* toxoid to control cellulitis in turkeys. *J. Appl. Poult. Res.* 21, 358–366.

Thammana, M. (2016). A Review on High Performance Liquid Chromatography (HPLC). *Res. Rev. J. Pharm. Anal. RRJPA* 5, 22–28. Available at: https://www.rroij.com/open-access/a-review-on-high-performance-liquid-chromatography-hplc-.pdf.

Therdtatha, P., Tandumrongpong, C., Pilasombut, K., Matsusaki, H., Keawsompong, S., and Nitisinprasert, S. (2016). Characterization of antimicrobial substance from *Lactobacillus salivarius* KL-D4 and its application as biopreservative for creamy filling. *Springerplus* 5. doi:10.1186/s40064-016-2693-4.

Timbermont, L., Haesebrouck, F., Ducatelle, R., and Van Immerseel, F. (2011). Necrotic enteritis
in broilers: An updated review on the pathogenesis. *Avian Pathol.* 40, 341-347.
doi:10.1080/03079457.2011.590967.

Todorov, S., Gotcheva, B., Dousset, X., Onno, B., and Ivanova, I. (2000). Influence of growth medium on bacteriocin production in *Lactobacillus plantarum* st31. *Biotechnol. Biotechnol. Equip.* 14, 50-55. doi:10.1080/13102818.2000.10819062.

Tsai, Y. T., Cheng, P. C., and Pan, T. M. (2012). The immunomodulatory effects of lactic acid bacteria for improving immune functions and benefits. *Appl. Microbiol. Biotechnol.* 96, 853-862. doi:10.1007/s00253-012-4407-3.

Tsiouris, V., Georgopoulou, I., Batzios, C., Pappaioannou, N., Ducatelle, R., and Fortomaris, P. (2015). The effect of cold stress on the pathogenesis of necrotic enteritis in broiler chicks. The effect of cold stress on the pathogenesis of necrotic enteritis in broiler chicks. *Avian Dis.* 44, 430-435. doi:10.1080/03079457.2015.1083094.

Tuomola, E. M., Ouwehand, A. C., and Salminen, S. J. (1999). Human ileostomy glycoproteins as a model for small intestinal mucus to investigate adhesion of probiotics. *Lett. Appl. Microbiol.* 28, 159-163. doi:10.1046/j.1365-2672.1999.00518.x.

Udaondo, Z., Duque, E., and Ramos, J.-L. (2017). The pangenome of the genus *Clostridium*. *Environ. Microbiol.* 19, 2588-2603. doi:10.1111/1462-2920.13732.

Uzal, F. A., Freedman, J. C., Shrestha, A., Theoret, J. R., Garcia, J., Awad, M. M., et al. (2014). Towards an understanding of the role of *Clostridium perfringens* toxins in human and animal disease. *Future Microbiol.* 9, 361-377.

Uzal, F. A., McClane, B. A., Cheung, J. K., Theoret, J., Garcia, J. P., Moore, R. J., et al. (2015). Animal models to study the pathogenesis of human and animal *Clostridium perfringens* infections. *Vet. Microbiol.* 179, 23-33. doi:10.1016/j.vetmic.2015.02.013.

Valerio, F., Lavermicocca, P., Pascale, M., and Visconti, A. (2004). Production of phenyllactic acid by lactic acid bacteria: an approach to the selection of strains contributing to food quality and preservation. *FEMS Microbiol. Lett.* 233, 289-295. doi:10.1016/j.femsle.2004.02.020.

Van Boeckel, T. P., Brower, C., Gilbert, M., Grenfell, B. T., Levin, S. A., Robinson, T. P., et al. (2015). Global trends in antimicrobial use in food animals. *PNAS* 112, 5649-5654. doi:10.1073/pnas.1503141112.

van Heel, A. J., de Jong, A., Montalbán-López, M., Kok, J., and Kuipers, O. P. (2013). BAGEL3: Automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides. *Nucleic Acids Res.* 41, 448-453. doi:10.1093/nar/gkt391.

Van Immerseel, F., De Buck, J., Pasmans, F., Huyghebaert, G., Haesebrouck, F., and Ducatelle, R. (2004). *Clostridium perfringens* in poultry: An emerging threat for animal and public health. *Avian Pathol.* 33, 537-549. doi:10.1080/03079450400013162.

Veillon, A., and Zuber, A. (1898). Recherches sur quelques microbes strictement anaérobies et leur role en pathologie. *Arch. Med. Exp. Anat. Pathol.* 10, 517-545.

Veljović, K., Popović, N., Miljković, M., Tolinački, M., Terzić-Vidojević, A., and Kojić, M. (2017). Novel aggregation promoting factor AggE contributes to the probiotic properties of *Enterococcus faecium* BGGO9-28. *Front. Microbiol.* 8, 1843. doi:10.3389/fmicb.2017.01843.

Ventura, M., O'Connell-Motherway, M., Leahy, S., Moreno-Munoz, J. A., Fitzgerald, G. F., and Sinderen, D. van (2007). From bacterial genome to functionality; case bifidobacteria. *Int. J. Food Microbiol.* 120, 2-12. doi:10.1016/j.ijfoodmicro.2007.06.011.

Verhoeckx, K., Cotter, P., López-Expósito, I., Kleiveland, C., Lea, T., Mackie, A., et al. (2015).
*The Impact of Food Bioactives on Gut Health*. Springer Cham Heidelberg New York Dordrecht London doi:10.1007/978-3-319-16104-4.

Vizoso Pinto, M. A. G., Schuster, T., Briviba, K., Watzl, B., Holzapfel, W. H., and A P Franz, C. M. (2007). Adhesive and Chemokine Stimulatory Properties of Potentially Probiotic *Lactobacillus* Strains. *J. Food Prot.* 70, 125–134. doi:10.4315/0362-028X-70.1.125.

Vlasova, A. N., Kandasamy, S., Chattha, K. S., Rajashekara, G., and Saif, L. J. (2016). Comparison of probiotic lactobacilli and bifidobacteria effects, immune responses and rotavirus vaccines and infection in different host species. *Vet. Immunol. Immunopathol.* 172, 72–84. doi:10.1016/j.vetimm.2016.01.003.

Vlková, E., Rada, V., Šmehilová, M., and Killer, J. (2008). Auto-aggregation and Co-aggregation ability in bifidobacteria and clostridia. *Folia Microbiol. (Praha)*. 53, 263–269. doi:10.1007/s12223-008-0040-z.

Vodnar, D. C., Paucean, A., Dulf, F. V., and Socaciu, C. (2010). HPLC characterization of lactic acid formation and FTIR fingerprint of probiotic bacteria during fermentation processes. *Not. Bot. Horti Agrobot. Cluj-Napoca* 38, 109–113. doi:10.15835/nbha3824752.

Vohra, A., Syal, P., and Madan, A. (2016). Probiotic yeasts in livestock sector. *Anim. Feed Sci. Technol.* 219, 31–47. doi:10.1016/j.anifeedsci.2016.05.019.

Wade, B., and Keyburn, A. (2015). The true cost of necrotic enteritis. *World Poult.* 31, 16–17.

Walter, J., Schwab, C., Loach, D. M., Gänzle, M. G., and Tannock, G. W. (2008). Glucosyltransferase A (GtfA) and inulosucrase (Inu) of *Lactobacillus reuteri* TMW1. 106 contribute to cell aggregation, in vitro biofilm formation, and colonization of the mouse gastrointestinal tract. *Microbiol. Res.* 154, 72–80. doi:10.1099/mic.0.2007/010637-0.

Wang, C., Chang, T., Yang, H., and Cui, M. (2014a). Surface physiological changes induced by lactic acid on pathogens in consideration of pKa and pH. *Food Control* 46, 525–531. doi:10.1016/j.foodcont.2014.06.024.

Wang, C., Chang, T., Yang, H., and Cui, M. (2015). Antibacterial mechanism of lactic acid on physiological and morphological properties of *Salmonella Enteritidis*, *Escherichia coli* and *Listeria monocytogenes*. *Food Control* 47, 231–236. doi:10.1016/j.foodcont.2014.06.034.

Wang, L., Fang, M., Hu, Y., Yang, Y., Yang, M., and Chen, Y. (2014b). Characterization of the most abundant *Lactobacillus* species in chicken gastrointestinal tract and potential use as probiotics for genetic engineering. *Acta Biochim Biophys Sin* 46, 612–619. doi:10.1093/abbs/gmu037.Advance.

Weber, T., Blin, K., Duddela, S., Krug, D., Kim, H. U., Bruccoleri, R., et al. (2015). antiSMASH 3.0 — a comprehensive resource for the genome mining of biosynthetic gene clusters. *Nucleic Acids Res.* 43, 237–243. doi:10.1093/nar/gkv437.

Weese, J. S., Reid-Smith, R. J., Avery, B. P., and Rousseau, J. (2010). Detection and characterization of *Clostridium difficile* in retail chicken. *Lett. Appl. Microbiol.* 50, 362–365. doi:10.1111/j.1472-765X.2010.02802.x.

Wenk, C., Pfirter, H. P., and Bickel, H. (1980). Energetic aspects of feed conversion in growing pigs. *Livest. Prod. Sci.* 7, 483–495. doi:10.1016/0301-6226(80)90086-X.

Werner, G., Coque, T. M., Hammerum, A. M., Hope, R., Hryniewicz, W., Johnson, A., et al. (2008). Emergence and spread of vancomycin resistance among Enterococci in Europe. *Eurosurveillance* 13, 1–11.

Wiegel, J., Tanner, R., Rainey, F.. (2006). “An Introduction to the family Clostridiaceae,” in *The Prokaryotes, Bacteria: Firmicutes, Cyanobacteria*, eds. M. Dworkin., S. Falkow., E. Rosenberg, K.-H. Schleifer, and E. Stackebrandt., 654–678.
Wieser, A., Schneider, L., Jung, J., and Schubert, S. (2012). MALDI-TOF MS in microbiological diagnostics-identification of microorganisms and beyond (mini review). *Appl. Microbiol. Biotechnol.* 93, 965-974. doi:10.1007/s00253-011-3783-4.

Wilkie, D. C., Kessel, A. G. Van, White, L. J., Laarveld, B., and Drew, M. D. (2005). Dietary amino acids affect intestinal *Clostridium perfringens* populations in broiler chickens. *Can. J. Anim. Sci.* 85, 185-193.

Williams, R. B. (2005). Intercurrent coccidiosis and necrotic enteritis of chickens: Rational, integrated disease management by maintenance of gut integrity. *Avian Pathol.* 34, 159-180. doi:10.1080/03079450500112195.

Wood, D. E., and Salzberg, S. L. (2014). Kraken: ultrafast metagenomic sequence classification using exact alignments. *Genome Biol.* 15, R46. doi:10.1126/science.1093857.

Wright, G. D. (2010). Q&A: Antibiotic resistance: Where does it come from and what can we do about it? *BMC Biol.* 8, 123. doi:10.1186/1741-7007-8-123.

Wu, S. B., Stanley, D., Rodgers, N., Swick, R. A., and Moore, R. J. (2014). Two necrotic enteritis predisposing factors, dietary fishmeal and *Eimeria* infection, induce large changes in the caecal microbiota of broiler chickens. *Vet. Microbiol.* 169, 188-197. doi:10.1016/j.vetmic.2014.01.007.

Wu, S., Rodgers, N., and Choct, M. (2011). Real-Time PCR Assay for *Clostridium perfringens* in Broiler Chickens in a Challenge Model of Necrotic Enteritis □. *Appl. Environ. Microbiol.* 77, 1135-1139. doi:10.1128/AEM.01803-10.

Yan, F., and Polk, D. B. (2012). Characterization of a probiotic-derived soluble protein which reveals a mechanism of preventive and treatment effects of probiotics on intestinal inflammatory diseases. *Gut Microbes* 3, 25-28.

Yan, X., Porter, C. J., Hardy, S. P., Steer, D., Smith, A. I., Quinsey, N. S., et al. (2013). Structural and Functional Analysis of the Pore-Forming Toxin NetB from *Clostridium perfringens*. *MBio* 4, e00019-13. doi:10.1128/mBio.00019-13 Editors.

Yang, C. M., Cao, G. T., Ferket, P. R., Liu, T. T., Zhou, L., Zhang, L., et al. (2012). Effects of probiotic, *Clostridium butyricum*, on growth performance, immune function, and cecal microflora in broiler chickens. *Poult. Sci.* 91, 2121-2129.

Yang, F., Hou, C., Zeng, X., and Qiao, S. (2015). The use of lactic acid bacteria as a probiotic in swine diets. *Pathogens* 4, 34-45. doi:10.3390/pathogens4010034.

Yirga, H. (2015). The use of probiotics in animal nutrition. *J. Probiotics Heal.* 3. doi:10.4172/2329-8901.1000132.

Yoo, J. Y., and Kim, S. S. (2016). Probiotics and Prebiotics: Present Status and Future. *Nutrients* 8, 173. doi:10.3390/nu8030173.

Zarate, G., Morata de Ambrosini, V. I., Perez Chaia, A., and Gonzalez, S. N. (2002). Adhesion of Dairy Propionibacteria to Intestinal Epithelial Tissue *In Vitro* and *In Vivo*. *J. Food Prot.* 65, 534-539.

Zeng, X., and Lin, J. (2017). Factors influencing horizontal gene transfer in the intestine. *Anim. Heal. Res. Rev.* 18, 153-159. doi:10.1017/S1466252317000159.

Zhang, W., Zhu, Y., Yang, J., Yang, G., Zhou, D., and Wang, J. (2015). A Selected *Lactobacillus rhamnosus* Strain Promotes EGFR-Independent Akt Activation in an Enterotoxigenic *Escherichia coli* K88- Infected IPEC-J2 Cell Model. *PLoS One* 10, e0125717. doi:10.1371/journal.pone.0125717.

Zhang, X., Liu, G., Zhao, B., and Li, P. (2012). New insight into the regulation of class II bacteriocin production by *quorum sensing* in *Lactobacillus pentosus* 31-1. *African J.*
*Microbiol. Res.* 6, 3582–3588. doi:10.5897/AJMR11.1147.

Zhitnitsky, D., Rose, J., and Lewinson, O. (2017). The highly synergistic, broad spectrum, antibacterial activity of organic acids and transition metals. *Nat. Publ. Gr.*, 1–13. doi:10.1038/srep44554.

Zhu, X. Y., Zhong, T., Pandya, Y., and Joerger, R. D. (2002a). 16S rRNA-based analysis of microbiota from the cecum of broiler chickens. *Appl. Environ. Microbiol.* 68, 124–137. doi:10.1128/AEM.68.1.124-137.2002.

Zhu, X. Y., Zhong, T., Pandya, Y., and Joerger, R. D. (2002b). 16S rRNA-Based Analysis of Microbiota from the Cecum of Broiler Chickens †. 68, 124–137. doi:10.1128/AEM.68.1.124.

Zhu, Y. H., Li, X. Q., Zhang, W., Zhou, D., Liu, H. Y., and Wang, J. F. (2014). Dose-dependent effects of *Lactobacillus rhamnosus* on serum interleukin-17 production and intestinal T-cell responses in pigs challenged with Escherichia coli. *Appl. Environ. Microbiol.* 80, 1787–1798. doi:10.1128/AEM.03668-13.

Zimmer, M., Vukov, N., Scherer, S., and Loessner, M. J. (2002). The Murein Hydrolase of the Bacteriophage □ 3626 Dual Lysis System Is Active against All Tested *Clostridium perfringens* Strains. *Appl. Environ. Microbiol.* 68, 5311–5317. doi:10.1128/AEM.68.11.5311.