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Chapter 38 : Probiotics and Prebiotics

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Abstract:

Probiotic bacteria have long been believed to influence general health and well-being through their association with the gastrointestinal tract (GIT) and its normal microbiota. The microbiotas of humans, animals, and fowl vary considerably with the architecture of their GITs. Species of microorganisms are located at different locations throughout the GIT and include strains that are either harmful or beneficial to the host depending on the circumstances and specific strains involved. Probiotic microorganisms typically designed for delivery in dairy foods are most often members of the or genus. This chapter discusses the effects of probiotics on GIT ecology, and deals with the appropriateness, technological suitability, competitiveness, and performance and functionality, as the criteria for selection of probiotic cultures. Prebiotics stimulate the growth and activity of beneficial bacteria in an individual’s intestinal microbiota. The best-known prebiotics are fructo-oligosaccharides derived from food sources. Production of designer prebiotics can offer multiple activities in retarding undesirable microorganisms, better promoting the native desirable microbiota, or stimulating the growth or activity of synbiotic cultures. Expansion of avenues for incorporation into appropriate food vehicles and improved stimulation of beneficial microfloras are some of the aspects that are good targets for development of prebiotics.

Citation: Pfeiler E, Klaenhammer T. 2013. Probiotics and Prebiotics, p 949-971. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch38
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Figure 38.1

Probiotic pioneers: (A) Elie Metchnikoff (1845–1916), (B) strain Shirota, and (C) species. doi:10.1128/9781555818463.ch38f1

Citation: Pfeiler E, Klaenhammer T. 2013. Probiotics and Prebiotics, p 949-971. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch38
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Image of Figure 38.2
Figure 38.2

Relations among the most abundant bacterial species. The network was deduced from the analysis of 155 bacterial species present in at least one individual at a genome coverage of ≥1%. Size of the nodes (circles) indicates species abundance over the cohort; width of the edges (lines connecting the circles) indicates the value of the Pearson correlation coefficient (only the 342 values above 0.4 or below –0.4 out of a total of 11,935 were used for the network). Red arrows identify common lactobacilli also used as probiotic cultures. Adapted from reference with permission from Macmillan Publishers Ltd. doi:10.1128/9781555818463.ch38f2

Citation: Pfeiler E, Klaenhammer T. 2013. Probiotics and Prebiotics, p 949-971. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch38
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Figure 38.3

Differences in species of bacteria in human feces of different ages. From reference . doi:10.1128/9781555818463.ch38f3

Citation: Pfeiler E, Klaenhammer T. 2013. Probiotics and Prebiotics, p 949-971. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch38
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Figure 38.4

Predominant colonic microorganisms categorized into potentially harmful or beneficial groups. Adapted from reference . doi:10.1128/9781555818463.ch38f4

Citation: Pfeiler E, Klaenhammer T. 2013. Probiotics and Prebiotics, p 949-971. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch38
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Figure 38.5

Heath benefits and suspected mechanisms of probiotics versus abiotics. IgE and IgA, immunoglobulins E and A. doi:10.1128/9781555818463.ch38f5

Citation: Pfeiler E, Klaenhammer T. 2013. Probiotics and Prebiotics, p 949-971. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch38
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Figure 38.6

Phylogenetic relationships among members of the complex, representing nine variable regions in the 16S rRNA gene used for phylogenetic identification and analysis. Adapted from references and . doi:10.1128/9781555818463.ch38f6

Citation: Pfeiler E, Klaenhammer T. 2013. Probiotics and Prebiotics, p 949-971. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch38
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Figure 38.7

DNA fingerprint of the predominant culture isolated from human feces before feeding with a probiotic, after feeding with , and 2 weeks after feeding was halted. SmaI-digested DNA fragments prepared from individual colonies were separated on a pulsed-field electrophoresis gel. doi:10.1128/9781555818463.ch38f7

Citation: Pfeiler E, Klaenhammer T. 2013. Probiotics and Prebiotics, p 949-971. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch38
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Figure 38.8

Genome atlas of NCFM. The atlas represents a circular view of the complete genome sequence of NCFM. The key on the right describes the single circles in the top-down-outermost-innermost direction, as follows. Circle 1 (innermost), GC-skew. Circle 2, Clusters of Orthologous Groups (COG) classification. Predicted open reading frames (ORFs) were analyzed using the COG database and grouped into five major categories: 1, information storage and processing; 2, cellular processes and signaling; 3, metabolism; 4, poorly characterized; 5, ORFs with uncharacterized COGs or no COG assignment. Circle 3, ORF orientation. ORFs in the sense orientation (ORF+) are shown in blue; ORFs oriented in the antisense direction (ORF–) are shown in red. Circle 4, BLAST similarities. Deduced amino acid sequences compared against the nonredundant (nr) database using gapped BLASTP (4a). Regions in blue represent unique proteins in NCFM, whereas highly conserved features are shown in red. The degree of color saturation corresponds to the level of similarity. Circle 5, G+C content deviation. Deviations from the average G+C content are shown in either green (low-GC spike) or orange (high-GC spike). A boxfilter was applied to visualize contiguous regions of low or high deviations. Circle 6, ribosomal machinery. tRNAs, rRNAs, and ribosomal proteins are shown as green, cyan, and red lines, respectively. Clusters of proteins are represented as colored boxes to maintain readability. Circle 7, mobile elements. Predicted transposases are shown as light purple dots, and phage-related integrases are shown as orange dots. Circle 8, stress response. Genes involved in the general stress response, including chaperones, and genes involved in heat shock, DNA repair, and pH regulation are shown as dark purple dots. Circle 9, peptide and amino acid utilization. Proteases and peptidases are shown as green dots, and non-sugar-related transporters are shown as light blue dots. Circle 10 (outermost), two-component regulators (2CRS). Each 2CRS is represented as a brown dot, consisting of a response regulator and a histidine kinase. In circles 7 to 10 each full dot represents one predicted ORF and stacked dots represent clusters of ORFs. Selected features representing single ORFs and ORF clusters are shown outside of circle 10 with bars indicating their absolute size. The origin and terminus of DNA replication are identified in green and red, respectively. Other features: SlpA and SlpB (S-layer proteins), CdpA (cell division protein [ ]), sugar utilization (sucrose, fructo-oligosaccharide [FOS], trehalose, and raffinose), LacE (phosphotransferase system-sugar transporter), BshA and BshB (bile salt hydrolases), Mub-909 to Mub-1709 (mucus-binding proteins; the numbers correspond to the La numbering scheme), FbpA (fibronectin-binding protein), Cfa (cyclopropane fatty acid synthase), Fibronectin_binding (fibronectin-binding protein cluster), EPS_cluster (exopolysaccharides), Lactacin_B (bacteriocin), pauLA-I to pauLA-III (potential autonomous units), and prLA-I and prLA-II (phage remnants). Reprinted from reference . doi:10.1128/9781555818463.ch38f8

Citation: Pfeiler E, Klaenhammer T. 2013. Probiotics and Prebiotics, p 949-971. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch38
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Tables

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Table 38.1

Examples of human probiotic species and strains with research documentation

Citation: Pfeiler E, Klaenhammer T. 2013. Probiotics and Prebiotics, p 949-971. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch38
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Table 38.2

Microorganisms reviewed by the Food and Drug Administration Center for Veterinary Medicine that were found to present no safety concerns when used in direct-fed microbials

Citation: Pfeiler E, Klaenhammer T. 2013. Probiotics and Prebiotics, p 949-971. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch38
Generic image for table
Table 38.3

Proposed health benefits and mechanisms of probiotics

Citation: Pfeiler E, Klaenhammer T. 2013. Probiotics and Prebiotics, p 949-971. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch38
Generic image for table
Table 38.4

Compilation of Cochrane Collaboration reports on clinical uses of probiotics

Citation: Pfeiler E, Klaenhammer T. 2013. Probiotics and Prebiotics, p 949-971. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch38
Generic image for table
Table 38.5

Desirable selection criteria for probiotic strains

Citation: Pfeiler E, Klaenhammer T. 2013. Probiotics and Prebiotics, p 949-971. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch38
Generic image for table
Table 38.6

Prebiotic compounds influencing members of the intestinal microflora

Citation: Pfeiler E, Klaenhammer T. 2013. Probiotics and Prebiotics, p 949-971. In Doyle M, Buchanan R (ed), Food Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555818463.ch38

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