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1 Copyright is owned by the Author of the thesis. Permission is given for a copy to be downloaded by an individual for the purpose of research and private study only. The thesis may not be reproduced elsewhere without the permission of the Author.

14 α

18 α

39 Microbacterium liquefaciens/oxydans Rhodococcus erythropolis lacticum Serratia liquefaciens/odorifera Lactobacillus casei/curvatus/mindensis Enterobacter gergoviae animalis/coryneformis/curvatus/delbrueckii Klebsiella ozaenae/oxytoca johnsonii/paracasei/paraplantarum Kocuria carniphila/kristinae/rhizophila plantarum/rhamnosus/amylovorus Frigoribacterium species Lactococcus lactis/garvieae Paracoccus species Enterococcus faecalis/gallinarum Micrococcus species saccharominimus Ochrobactrum anthropi/tritici Chryseobacterium species Pantoea agglomerans Propionibacterium freudenreichii/jensenii Providencia stuartii Psychrobacter maritimus Staphylococcus capitis/cohnii Pseudoclavibacter helvolus saprophuticus/equorum/xylosus/aureus Rahnella aquatilis haemolyticus/hominis/epidermis Renibacterium salmoninarum Streptococcus uberis/parauberis Sphingomonas species Pseudomonas alcalophila/stutzeri Achromobacter delicatulus synxantha/fluorescens/putida Aeromonas hydrophila Corynebacterium ammoniagenes/freneyi Arthrobacter arilaitensis/psychrolactophilus glutamicum/variabilis/casei Brachybacterium nesterenkovii Acinetobacter johnsonii/junii/haemolyticus Deinococcus species lwoffii Dermacoccus species Leuconostoc mesenteroides Escherichia coli Aerococcus viridans Bacillus cereus Brevibacterium helvolum/linens

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72 D Simpson = ( n i 1) NN 1 i n i ( )

73 D Simpsonindexofdiversity = 1 ( n i 1) NN 1 ( ) i n i n i D Shannon = N.ln n i N i R = S 1 ln N

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198 > bact.glmer <- lmer(nscore ~ Trt*Milk_Type+(1 Date/Farm/Iso_rep)+(1 Media)+(1 Growth_Time), family=binomial, data=bact) > Anova(bact.glmer) Analysis of Deviance Table (Type II Wald chisquare tests) Response: nscore Chisq Df Pr(>Chisq) Trt < 2.2e-16 *** Milk_Type < 2.2e-16 *** Trt:Milk_Type *** --- Signif. codes: 0 *** ** 0.01 * > predictmeans(bact.glmer, "Trt:Milk_Type", Df=68.21, trans=invlogit) $`Predicted Means` Milk_Type Acid Raw Trt ph ph 2.5+Milk $`Standard Error of Means` Milk_Type Acid Raw Trt ph ph 2.5+Milk $`Standard Error of Differences` Max.SED Min.SED Aveg.SED attr(,"for the Same Level of Factor") Trt Milk_Type Aveg.SED Min.SED Max.SED $LSD Max.LSD Min.LSD Aveg.LSD attr(,"significant level") [1] 0.05 attr(,"degree of freedom") [1] $`Back Transformed Means` Trt Milk_Type Mean LL of 95% CI UL of 95% CI 1 ph 2.5 Acid ph 2.5 Raw ph 2.5+Milk Acid

199 4 ph 2.5+Milk Raw > predictmeans(bact.glmer, "Trt:Milk_Type", Df=68.21, trans=invlogit) $`Predicted Means` Milk_Type Acid Raw Trt ph ph 2.5+Milk ph 2.5+Salt $`Standard Error of Means` Milk_Type Acid Raw Trt ph ph 2.5+Milk ph 2.5+Salt $`Standard Error of Differences` Max.SED Min.SED Aveg.SED attr(,"for the Same Level of Factor") Trt Milk_Type Aveg.SED Min.SED Max.SED $LSD Max.LSD Min.LSD Aveg.LSD attr(,"significant level") [1] 0.05 attr(,"degree of freedom") [1] $`Back Transformed Means` Trt Milk_Type Mean LL of 95% CI UL of 95% CI 1 ph 2.5 Acid ph 2.5 Raw ph 2.5+Milk Acid ph 2.5+Milk Raw ph 2.5+Salt Acid ph 2.5+Salt Raw

200 Leuconostoc lactis Leuconostoc lactis Leuconostoc lactis Microbacterium phyllosphaerae or foliorum Staphylococcus haemolyticus Leuconostoc lactis Lactococcus lactis Lactobacillus paracasei Lactococcus lactis Lactococcus lactis Lactococcus lactis Curtobacterium flaccumfaciens Leuconostoc lactis Bacillus licheniformis Pseudomonas rhizosphaerae Curtobacterium flaccumfaciens Kocuria varians Lactococcus lactis Lactococcus lactis

201 Rathayibacter festucae Staphylococcus haemolyticus Plantibacter flavus Staphylococcus haemolyticus Bacillus licheniformis Arthrobacter citreus Kocuria varians

202 Staphylococcus haemolyticus Staphylococcus devriesei Leuconostoc lactis Leuconostoc lactis Staphylococcus aureus Leuconostoc lactis Leuconostoc lactis Lactococcus lactis Lactobacillus paracasei Curtobacterium flaccumfaciens Leuconostoc lactis Staphylococcus devriesei Bacillus licheniformis Pseudomonas moraviensis Pseudomonas moraviensis Curtobacterium flaccumfaciens Kocuria varians Lactococcus lactis Lactococcus lactis Rathayibacter festucae Staphylococcus haemolyticus Plantibacter flavus Staphylococcus haemolyticus Bacillus licheniformis

203 Arthrobacter citreus Kocuria varians

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Copyright is owned by the Author of the thesis. Permission is given for a copy to be downloaded by an individual for the purpose of research and

Copyright is owned by the Author of the thesis. Permission is given for a copy to be downloaded by an individual for the purpose of research and private study only. The thesis may not be reproduced elsewhere