Isaacson R, Kim HB. The intestinal microbiome of pigs. Anim Health Res Rev. 2012;13:100–9.
Article
PubMed
Google Scholar
Kim HB, Borewicz K, White BA, Singer RS, Sreevatsan S, Tu ZJ, et al. Longitudinal investigation of the age-related bacterial diversity in the feces of commercial pigs. Vet Microbiol. 2011;153:124–33.
Article
PubMed
Google Scholar
Niederwerder MC. Role of microbiome in swine respiratory disease. Vet Microbiol. 2017;209:97–106.
Article
CAS
PubMed
Google Scholar
Han GG, Lee JY, Jin GD, Park J, Choi YH, Kang SK, et al. Tracing of the fecal microbiota of commercial pigs at five growth stages from birth to shipment. Sci Rep. 2018;8:6012. https://doi.org/10.1038/s41598-018-24508-7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Holman DB, Brunelle BW, Trachsel J, Allen HK. Meta-analysis to define a core microbiota in the swine gut. mSystems. 2017;2(3):e00004–17. https://doi.org/10.1128/mSystems.00004-17.
Article
CAS
PubMed
PubMed Central
Google Scholar
Urubschurov V, Janczyk P, Souffrant WB, Freyer G, Zeyner A. Establishment of intestinal microbiota with focus on yeasts of unweaned and weaned piglets kept under different farm conditions. FEMS Microbiol Ecol. 2011;77:493–502.
Article
CAS
PubMed
Google Scholar
Shan T, Li L, Simmonds P, Wang C, Moeser A, Delwart E. The fecal virome of pigs on a high-density farm. J Virol. 2011;85:11697–708.
Article
CAS
PubMed
PubMed Central
Google Scholar
Castanon JIR. History of the use of antibiotics as growth promoters in European poultry feeds. Poult Sci. 2007;86:2466–71.
Article
CAS
PubMed
Google Scholar
Millet S, Maertens S. The European ban on antibiotic growth promoters in animal feed: from challenges to opportunities. Vet J. 2011;187:143–4.
Article
PubMed
Google Scholar
An official website of the European Union. (https://ec.europa.eu) Accessed on 24 Oct 2018.
Shim SB, Verstegen MW, Kim IH, Kwon OS, Verdonk JM. Effects of feeding antibiotic-free creep feed supplemented with oligofructose, probiotics or synbiotics to suckling piglets increases the preweaning weight gain and composition of intestinal microbiota. Arch Anim Nutr. 2005;59(6):419–27.
Article
CAS
PubMed
Google Scholar
Jacela JY, DeRouchey JM, Tokach MD, Goodband RD, Nellsen JL, Renter DG, et al. Feed additives for swine: fact sheets – acidifiers and antibiotics. J Swine Health Prod. 2009;17:270–5.
Google Scholar
Szuba-Trznadel A, Rząsa A, Lira R, Fuchs B. The influence of (1,3)-(1,6)-ß-D-glucan on the production results of sows and their offspring. J Anim Feed Sci. 2014;23(3):228–35.
Article
Google Scholar
Liu Y, Espinosa CD, Abeilla JJ, Casas GA, Lagos LV, Kwon WB, et al. Non-antibiotic feed additives in diets for pigs – a review. Anim Nutr. 2018;4:113–25.
Article
PubMed
PubMed Central
Google Scholar
Hanczakowska E, Swiatkiewicz M. Effect of herbal extracts on piglet performance and small intestinal epithelial villi. Czeh J Anim Sci. 2012;57(9):420–9.
Article
CAS
Google Scholar
Mehdi Y, Letourneau-Montminy MP, Goucher ML, Chorfi Y, Suresh G, Rouissi T, et al. Use of antibiotics in broiler production: global impacts and alternatives. Anim Nutr. 2018;4(2):170–8.
Article
PubMed
PubMed Central
Google Scholar
Tatara MR, Sliwa E, Dudek K, Gawron A, Piersiak T, Dobrowolski P, et al. Aged garlic extract and allicin improve performance and gastrointestinal tract development of piglets reared in artificial sow. Ann Agric Environ Med. 2008;15:63–9.
CAS
PubMed
Google Scholar
Lee DH, Ra CS, Song YH, Sung KI, Kim JD. Effects of dietary garlic extract on growth, feed utilization and whole body composition of juvenile Sterlet sturgeon (Acipenser ruthenus). Asian Australas J Anim Sci. 2012;25(4):577–83. https://doi.org/10.5713/ajas.2012.12012.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cheng G, Hao H, Xie S, Wang X, Dai M, Huang L, et al. Antibiotic alternatives: the substitution of antibiotics in animal husbandry? Front Microbiol. 2014. https://doi.org/10.3389/fmicb.2014.00217.
Noman ZA, Hasan MM, Talukder S, Sarker YA, Paul TK, Sikder MH. Effect of garlic extract on growth, carcass characteristics and haematological parameters in broilers. Bangladesh Vet. 2015;32(1):1–6.
Google Scholar
Senthilkumar S, Madesh N, Purushothaman MR, Vasanthakumar P, Thirumalaisamy G, Sasikumar P. Effect of garlic supplementation on performance in broilers – a review. Int J Sci Environ Technol. 2015;4:980–3.
Google Scholar
Brzóska F, Śliwiński B, Michalik-Rutkowska O, Śliwa J. The effect of garlic (allium sativum L) on growth performance, mortality rate, meat and blood parameters in broilers. Ann Anim Sci. 2015;15(4):961–75.
Article
CAS
Google Scholar
Sheoran N, Kumar R, Kumar A, Batra K, Sihag S, Maan S, et al. Nutrigenomic evaluation of garlic (Allium sativum) and holy basil (Ocimum sanctum) leaf powder supplementation on growth performance and immune characteristics in broilers. Veterinary World. 2017;10(1):121–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu Y, Che TM, Song M, Lee JJ, Almeida JA, Bravo D, et al. Dietary plant extracts improve immune response and growth efficiency of pigs experimentally infected with porcine reproductive and respiratory syndrome virus. J Anim Sci. 2013;91(12):5668–79.
Article
CAS
PubMed
Google Scholar
Yan L, Meng QW, Kim IH. Effects of fermented garlic powder supplementation on growth performance, nutrient digestibility, blood characteristics and meat quality in growing-finishing pigs. Anim Sci J. 2012;85(5):411–7. https://doi.org/10.1111/j.1740-0929.2011.00973.x.
Article
CAS
Google Scholar
Adebiyi OA, Ajayi OS, Adejumo IO, Osungade TO. Performance, microbial load and gut morphology of weaned pigs fed diets supplemented with turmeric, ginger and garlic extracts. Trop Anim Prod Invest. 2014;17(1):25–31.
Google Scholar
Estienne MJ, Harstock TG, Harper AF. Effects of antibiotics and probiotics on suckling pig and weaned pig performance. Int J Appl Res Vet Med. 2005;3(4):303–8.
Google Scholar
Szabó I, Wieler LH, Tedin K, Scharek-Tedin L, Taras D, Hensel A, et al. Influence of a probiotic strain of enterococcus faecium on salmonella enterica serovar Typhimurium DT104 infection in a porcine animal infection model. Appl Environ Microbiol. 2009;96:219–33.
Google Scholar
Liao SF, Nyachoti M. Using probiotics to improve swine gut health and nutrient utilization. Anim Nutr. 2017;3(4):331–43.
Article
PubMed
PubMed Central
Google Scholar
Markowiak P, Śliżewska K. The role of probiotics, prebiotics and synbiotics in animal nutrition. Gut Pathogens. 2018;10:21. https://doi.org/10.1186/2Fs13099-018-0250-0.
Article
PubMed
PubMed Central
Google Scholar
De Cupere F, Deprez P, Demeulenaere D, Muylle E. Evaluation of the effect of 3 probiotics on experimental Escherichia coli enterotoxaemia in weaned piglets. J Vet Med B. 1992;39:277–84.
Article
Google Scholar
Kreuzer S, Janczyk P, Assmus J, Schmidt MFG, Brockmann GA, Nöckler K. No beneficial effects evident for enterococcus faecium NCIMB 10415 in weaned pigs infected with salmonella enterica serovar Typhimurium DT104. Appl Environ Microbiol. 2012;78:4816–25.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dowarah R, Agarwal AKVN. The use of lactobacillus as an alternative of antibiotic growth promoters in pigs. Anim Nutr. 2017;3(1):1–6. https://doi.org/10.1016/j.aninu.2016.11.002.
Article
PubMed
Google Scholar
Napiórkowska B, Dobrowolska Z, Więcek J, Gajewska J, Rekiel A. Effect of a probiotic preparation on daily weight gain, survival rate and composition of faecal microflora in piglets (in Polish). Roczniki Naukowe Polskiego Towarzystwa Zootechnicznego. 2014;10(1):57–68.
Google Scholar
Zeyner A, Boldt E. Effects of probiotic Enterococcus faecium strain suplemmented from birth to weaning on diarrhoea patterns and performance of piglets. J Anim Physiol Anim Nutr. 2006;90(1–2):25–31.
Article
CAS
Google Scholar
Brzozowski B, Bednarski W, Gołek P. The adhesive capability of two lactobacillus strains and physicochemical properties of their synthesized biosurfactants. Food Technol Biotechnol. 2011;49(2):177–86.
CAS
Google Scholar
Zhang L, Xu Y, Liu H, Lai T, Ma J, Wang J, et al. Evaluation of Lactobacillus rhamnosus GG using an Escherichia coli K88 model of piglet diarrhoea: effects on diarrhoea incidence, faecal microflora and immune responses. Vet Microbiol. 2010;141(1–2):142–8.
Article
CAS
PubMed
Google Scholar
Cai CJ, Cai PP, Hou CL, Zeng XF, Qiao SY. Administration of Lactobacillus fermentum I5007 to young piglets improved their health and growth. J Anim Feed Sci. 2014;23(3):222–7.
Article
Google Scholar
Kim HB, Borewicz K, Whiteb BA, Singera RS, Sreevatsana S, Tuc ZJ, et al. Microbial shifts in the swine distal gut in response to the treatment with antimicrobial growth promoter, tylosin. PNAS. 2012;109(38):15485–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
McCormack UM, Curião T, Wilkinson T, Metzler-Zebeli BU, Reyer H, Ryan T, et al. Fecal microbiota transplantation in gestating sows and neonatal offspring alters lifetime intestinal microbiota and growth in offspring. mSystems. 2018;3(3):e00134–17. https://doi.org/10.1128/mSystems.00134-17.
Article
CAS
PubMed
PubMed Central
Google Scholar
Quan J, Cai G, Ye J, Yang M, Ding R, Wang X, et al. A global comparison of the microbiome compositions of three gut locations in commercial pigs with extreme feed conversion ratios. Sci Rep. 2018;8:4536. https://doi.org/10.1038/s41598-018-22692-0.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brässen C, Esser D, Rauch B, Siebers B. Carbohydrate metabolism in Archaea. Current insights into unusuall enzymes and pathways and their regulation. Microbiol Mol Biol Rev. 2014;78(1):89–175.
Article
CAS
Google Scholar
Thauer RK, Kaster AK, Seedorf H, Buckel W, Hedderich L. Methanogenic archaea: ecologically relevant differences in energy conservation. Nat Rev Microbiol. 2008;6(8):579–91.
Article
CAS
PubMed
Google Scholar
Jabłoński S, Rodowicz P, Łukaszdewicz M. Methanogenic Archaea database containing physiological and biochemical characteristics. Int J Syst Evol Microbiol. 2015;65:1360–8.
Article
PubMed
CAS
Google Scholar
Brugère JF, Borrel G, Gaci N, Tottey W, O’Tole PW, Malpuech-Brugère C. Archaebiotics: proposed therapeutic use of archaea to prevent trimethylaminuria and cardiovascular disease. Gut Microbes. 2014;5(1):5–10. https://doi.org/10.4161/gmic.26749.
Article
PubMed
Google Scholar
Brugère JF, Ben Hania W, Arnal ME, Ribière C, Ballet N, Vandeckerkove P, et al. Archaea: microbial candidates in next generation probiotics development. J Clin Gastroenterol. 2017;52(Suppl 1):S71–3. https://doi.org/10.1097/MCG.0000000000001043 Proceedings from the 9th Probiotics, Prebiotics and New Foods, Nutraceuticals and Botanicals for Nutrition & Human and Microbiota Health Meeting: 10 to 12 September 2017; Rome.
Article
Google Scholar
La Reau AJ, Meier-Kolthoff JP, Suen G. Sequence-based analysis of the genus Ruminococcus resolves its phylogeny and reveals strong host association. Microbial Genomics. 2016;2. https://doi.org/10.1099/mgen.0.000099.
Ze X, Duncan SH, Louis P, Flint HJ. Ruminococcus bromii is a keystone species for the degradation of resistant starch in human colon. ISME J. 2012;6:1535–43.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kovatcheva-Datchary P, Nillson A, Akrami R, Lee YS, De Vadder F, Arora T, et al. Dietetary fiber-induced improvement in glucose metabolism is associated with increased abundance of Prevotella. Cell Metab. 2015;22:971–82.
Article
CAS
PubMed
Google Scholar
Frese SA, Parker K, Calvert CC, Mills DA. Diet shapes the gut microbiome of pigs during nursing and weaning. Microbiome. 2015;3(28). https://doi.org/10.1186/s40168-015-0091-8.
Flint HJ, Bayer EA, Rincon MT, Lamed R, White BA. Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Nat Rev Microbiol. 2008;6:121–31.
Article
CAS
PubMed
Google Scholar
Vital M, Howe AC, Tjedje JM. Revealing the bacterial butyrate synthesis pathways by analyzing meta (genomic) data. mBio. 2014;5(2):e00889. https://doi.org/10.1128/mBio.00889-14.
Article
PubMed
PubMed Central
Google Scholar
Cassir N, Benamar B, La Scola B. Clostridium butyricum: from benefitial to a new emerging pathogen. Clin Microbiol Infect. 2016;22:37–45.
Article
PubMed
Google Scholar
Poduval RD, Mohandas R, Unnikrishnan D, Corpuz M. Clostridium Cadaveris Bactereia in an Immunocompetent host. Clin Infect Dis. 1999;29(1):1354–5.
Article
CAS
PubMed
Google Scholar
Xianhua C, Xiaoli L, Xsiuzhu D. Alcaliphilus crotonatoxidans sp. nov., a strictly anaerobic, crotonate-dysmutating bacterium isolated from a methanogenic environment. Int J Syst Evol Microbiol. 2003;53(4):971–5.
Article
CAS
Google Scholar
Goldstein EJC, Tyrrell KL, Citron DM. Lactobacillus species: taxonomic complexity and controversial susceptibilities. Clin Infect Dis. 2015;60(2):98–107.
Article
CAS
Google Scholar
Azad AK, Sarker M, Li T, Yin J. Probiotic species in the modulation of gut microbiota, an overview. Biomed Res Int. 2018. https://doi.org/10.1155/2018/9478630.
Walter J. Ecological role of lactobacilli in the gastrointestinal tract: implication for fundamental and biomedical research. Appl Environ Microbiol. 2018;74(16):4985–96.
Article
CAS
Google Scholar
Govender M, Choonara YE, Kumar P, du Toit LC, van Vuuren S, Pillay V. A review of the advancements in probiotic delivery: conventional vs. non-conventional formulations for intestinal flora supplementation. J Am Assoc Pharmaceut Scientists. 2013;15(1):29–43.
Google Scholar
Hou C, Zeng X, Yang F, Liu H, Qiao S. Study and use of the probiotic lactobacillus reuteri in pigs: a review. J Anim Sci Biotechnol. 2015;6(1):14.
Article
PubMed
PubMed Central
CAS
Google Scholar
Vasquez N, Suau A, Magne F, Pochart P, Pélissier M. Differential effects of Bifidobacterium pseudolongum strain Patronus and metronidazole in the rat gut. Physiol Biotechnol. 2009;75(2):381–6.
CAS
Google Scholar
Looft T, Johnsonb TA, Allena HK, Baylesa DO, Alta DP, Stedtfeld RD, et al. In-feed antibiotic effects on the swine intestinal microbiome. PNAS. 2012;109(5):1691–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Soler C, Goossens T, Bermejo A, Migura-Garcia L, Cusco A, Francino O, et al. Digestive microbiota is different in pigs receiving antimicrobials or feed additive during the nursery period. PLoS One. 2016;13(5):e0197353. https://doi.org/10.1371/journal.pone.0197353.
Article
CAS
Google Scholar
Wexler AG, Goodman AL. An insider’s perspective: Bacteroides as a window into the microbiome. Nat Microbiol. 2017;2:17026. https://doi.org/10.1038/nmicrobiol.2017.26.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bin P, Tang Z, Lju S, Chen S, Xia Y, Liu J, et al. Intestinal microbiota mediates Enterotoxigenic Escherichia coli-induced diarrhea in piglets. BMC Vet Res. 2018;14:385. https://doi.org/10.1186/s.12917-018-1704-9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Goyette-Desjardins G, Auger JP, Xu J, Segura M, Gottschalk M. Streptococcus suis, an important pig pathogen and emerging zoonotic agent-an update on the worldwide distribution based on serotyping and sequence typing. Emerg Microbes Infect. 2014;3:6. https://doi.org/10.1038/emi.2014.45.
Article
Google Scholar
Aalbaeck B, Christensen H, Bisqaard M, Lijegren CH, Nielsen OL, Jensen HE. Actinomyces hyovaginalis associated with disseminated necrotic lung lesions in slaughter pigs. J Comp Pathol. 2003;129(1):70–7.
Article
Google Scholar
Deng H, Li Z, Tan Y, Guo Z, Liu Y, Wang Y, et al. A novel strain of Bacteroides fragilis enhances phagocytosis and polarises M1 macrophages. Sci Rep. 2016;6:1–11.
Article
CAS
Google Scholar
Myers LL, Shoop DS. Association of enterotoxigenic Bacteroides fragilis with diarrheal disease in young pigs. Am J Vet Res. 1987;48(5):774–5.
CAS
PubMed
Google Scholar
Bag S, Ghosh TS, Dascorresponding B. Complete genome sequence of Collinsella aerofaciens isolated from the gut of a healthy Indian subject. Genome Announc. 2017;5(47):e01361–17.
Article
PubMed
PubMed Central
Google Scholar
Wendt M, Liebhold M, Kaup F, Amtsberg G, Bollwahn W. Corynebacterium suis infection in swine 1, clinical diagnosis with special considereation of urine studies and cystoscopy. Tieraerztliche Praxix. 1990;18(4):353–7.
CAS
Google Scholar
Bernard K. The genus corynebacterium and other medically relevant coryneform-like bacteria. J Clin Microbiol. 2012. https://doi.org/10.1128/JCM.00792-12.
Sengupta M, Naina P, Balaji V, Anandan S. Corynebacterium amycolatum: an unexpected pathogen in the ear. J Clin Diagn Res. 2015;9(12):DD01–3.
CAS
PubMed
PubMed Central
Google Scholar
Hernandez-Leon F, Acosta-Dibarrat J, Vasquez-Chagoyan JC, Fernandes Rosas P, Montes de Oca-Jimenez R. Identification and molecular characterization of Corynebacterium xerosis isolated from a sheep cutaneous abscess: first case report in Mexico. BMC Res Notes. 2016;9:358. https://doi.org/10.1186/s13104-016-2170-8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tong J, Han Q, Wang S, Su Z, Zheng D, Shen P, et al. Corynebacterium pyruviciproducens, as an immune modulator, can promote the activity of macrophages and up-regulate antibody response to particulate antigen. Exp Biol Med. 2012;237(11):1322–30.
Article
CAS
Google Scholar
Kraatz M, Wallace RJ, Svensson L. Olsenella umbonata sp. nov., a microaerotolerant anaerobic lactic acid bacterium from the sheep rumen and pig jejunum, and emended descriptions of Olsenella, Olsenella uli and Olsenella profusa. Int J Syst Evol Microbiol. 2011;61:795–803.
Article
CAS
PubMed
Google Scholar
Modolo JR, Margato LFF, Gottschalk AF, de Magalhaes Lopez CA. Incidence of campylobacter in pigs with and without diarrhea. Rev Microbiol. 1999;30:19–21.
Article
Google Scholar
An official website of the European Union [https://ec.europa.eu/food/sites/food/files/safety/docs/animal-feed-eu-reg-comm_register_feed_additives_1831-03.pdf.] Accessed on 24 Oct 2018.
Ferris MJ, Muyzer G, Ward DM. Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl Environ Microbiol. 1996;62:340–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jost L. Entropy and diversity. OIKOS. 2006;113(2):363–75.
Article
Google Scholar