Bacillus and Paenibacillus spp. associated with extended shelf life milk

TL;DR: This review focuses on milk processing techniques used to identify microorganisms associated with milk pathogenicity and outbreaks, as well as their applications in food production and consumption.

Abstract: ................................................................................................................................... ii DEDICATION ............................................................................................................................... iv ACKNOWLEDGEMENTS ............................................................................................................ v TABLE OF CONTENTS ............................................................................................................... vi LIST OF TABLES ........................................................................................................................ xii LIST OF FIGURES ..................................................................................................................... xiii CHAPTER ONE ............................................................................................................................. 1 GENERAL INTRODUCTION ....................................................................................................... 1 CHAPTER TWO ............................................................................................................................ 5 LITERATURE REVIEW ............................................................................................................... 5 2.1 Milk production and consumption trends ........................................................................ 6 2.2 Extended shelf life milk ................................................................................................... 8 2.2.1 Milk chilling............................................................................................................ 10 2.2.2 Heat treatment of milk ............................................................................................ 11 2.2.2.1 Pasteurisation of milk ...................................................................................... 12 2.2.3 Microfiltration of milk ............................................................................................ 14 2.2.4 Bactofugation of milk ............................................................................................. 15 2.2.5 Aseptic packaging ................................................................................................... 16 vii 2.3 Bacteria associated with milk ......................................................................................... 17 2.3.1 Raw milk ................................................................................................................. 17 2.3.2 Heat treated milk ..................................................................................................... 19 2.3.2.1 Pasteurised milk ............................................................................................... 19 2.3.2.2 ESL milk .......................................................................................................... 20 2.4 Contamination routes in milk processing ....................................................................... 21 2.4.1 Milk at the farm ...................................................................................................... 21 2.4.1.1 Interior of the udder ......................................................................................... 21 2.4.1.2 Exterior of the udder ........................................................................................ 22 2.4.1.3 Water ............................................................................................................... 22 2.4.1.4 Milk handling equipment................................................................................. 23 2.4.2 Milk at the processing plant .................................................................................... 23 2.4.2.1 Processing equipment ...................................................................................... 23 2.4.2.2 Air in the processing plant ............................................................................... 24 2.4.2.3 Packaging materials ......................................................................................... 24 2.5 Adaptation mechanisms of bacteria during milk processing ......................................... 25 2.5.1 Bacterial endospores ............................................................................................... 26 2.5.2 Biofilms................................................................................................................... 27 2.5.3 Cold shock response ............................................................................................... 28 2.6 Spore-forming bacteria associated with ESL milk ......................................................... 30 2.6.1 Paenibacillus spp. ................................................................................................... 30 2.6.2 Bacillus spp. ............................................................................................................ 31 2.6.2.1 B. pumilus ........................................................................................................ 32 viii 2.6.2.2 B. subtilis ......................................................................................................... 33 2.6.2.3 B. cereus .......................................................................................................... 34 2.6.2.3.1 B. cereus pathogenicity and outbreaks ........................................................ 35 2.7 Advances in detection and identification of microorganisms in the food industry ........ 39 2.7.1 Protein based methods ............................................................................................ 39 2.7.1.1 Matrix Assisted Laser Desorption / Ionization Time of Flight Mass Spectrometry (MALDI-TOF-MS) .................................................................................... 39 2.7.2 DNA based methods ............................................................................................... 40 2.7.2.1 End point PCR ................................................................................................. 40 2.7.2.2 rep-PCR ........................................................................................................... 40 2.7.2.3 16S sequencing ................................................................................................ 41 2.7.3.4 Multilocus sequence typing (MLST) ............................................................... 42 2.7.3.5 Whole genome sequencing (WGS) ................................................................. 43 CHAPTER THREE ...................................................................................................................... 45 HYPOTHESES AND OBJECTIVES ........................................................................................... 45 3.1 Hypothesis 1 ................................................................................................................... 46 3.1.1 Objective ........................................................................................................................ 46 3.2 Hypothesis 2 ................................................................................................................... 47 3.2.1 Objective ........................................................................................................................ 47 CHAPTER FOUR ......................................................................................................................... 48 Bacillus and Paenibacillus spp. associated with extended shelf life milk during processing and storage ....................................................................................................................................... 48