Lactic Acid Bacteria: Fundamentals and Practice

536 Pages·2014·8.04 MB·English

by  Heping Zhang

Heping Zhang
Yimin Cai Editors
Lactic Acid
Bacteria
Fundamentals and Practice
Lactic Acid Bacteria
Heping Zhang Yimin Cai
•
Editors
Lactic Acid Bacteria
Fundamentals and Practice
123
Editors
Heping Zhang Yimin Cai
KeyLaboratory ofDairy Biotechnology Crop,Livestock and EnvironmentDivision
andEngineering, Ministry of Education JapanInternational Research Center
InnerMongolia AgriculturalUniversity forAgriculturalSciences
Hohhot Tsukuba
China Japan
ISBN 978-94-017-8840-3 ISBN 978-94-017-8841-0 (eBook)
DOI 10.1007/978-94-017-8841-0
Springer Dordrecht Heidelberg New YorkLondon
LibraryofCongressControlNumber:2014934661
(cid:2)SpringerScience+BusinessMediaDordrecht2014
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Contents
1 Phylogenesis and Evolution of Lactic Acid Bacteria. . . . . . . . . . . . 1
Zhihong Sun, Jie Yu, Tong Dan, Wenyi Zhang and Heping Zhang
2 Biodiversity of Lactic Acid Bacteria . . . . . . . . . . . . . . . . . . . . . . . 103
Wenjun Liu, Huili Pang, Heping Zhang and Yimin Cai
3 Genomics of Lactic Acid Bacteria. . . . . . . . . . . . . . . . . . . . . . . . . 205
Wenyi Zhang and Heping Zhang
4 Proteomics of Lactic Acid Bacteria. . . . . . . . . . . . . . . . . . . . . . . . 249
Rina Wu and Jing Lu
5 Lactic Acid Bacteria in Health and Disease. . . . . . . . . . . . . . . . . . 303
Jinzhong Xiao, Yong Zhang and Zhennai Yang
6 Lactic Acid Bacteria and the Human Gastrointestinal Tract . . . . . 375
Lai-yu Kwok
7 Application of Lactic Acid Bacteria for Animal Production. . . . . . 443
Yimin Cai, Huili Pang, Zhongfang Tan, Yanping Wang,
Jianguo Zhang, Chuncheng Xu, Jinsong Yang and Yang Cao
8 Traditional Chinese Fermented Dairy Foods. . . . . . . . . . . . . . . . . 493
Heping Zhang, Xia Chen, Tong Dan and Jie Dong
v
Contributors
Yimin Cai Crop, Livestock and Environment Division, Japan International
Research Centre for Agricultural Sciences, 1-1 Ohwashi, Ibaragi, Tsukuba 305-
8686, Japan, e-mail: [email protected]
Yang Cao BaYi Agricultural University, Mishan, China, e-mail: hbdkcaoyang@
163.com
Xia Chen Key Laboratory of Dairy Biotechnology and Engineering, Ministry of
Education, Inner Mongolia Agricultural University, Hohhot, China, e-mail:
[email protected]
TongDan KeyLaboratoryofDairyBiotechnologyandEngineering,Ministryof
Education, Inner Mongolia Agricultural University, Hohhot, China, e-mail:
[email protected]
JieDong InnerMongoliaNormalUniversity,Hohhot,China,e-mail:djnmdongjie@
126.com
Lai-yuKwok KeyLaboratoryofDairyBiotechnologyandEngineering,Ministry
of Education, Inner Mongolia Agricultural University, Hohhot, China, e-mail:
[email protected]
Wenjun Liu Key Laboratory of Dairy Biotechnology and Engineering, Ministry
of Education, Inner Mongolia Agricultural University, Hohhot, China, e-mail:
[email protected]
Jing Lu Chinese Academy of Agricultural Sciences, Institute of Agro-products
Processing Science and Technology, Beijing, China, e-mail: [email protected]
Huili Pang Zhengzhou University, Zhengzhou, China, e-mail: [email protected]
ZhihongSun KeyLaboratoryofDairyBiotechnologyandEngineering,Ministry
of Education, Inner Mongolia Agricultural University, Hohhot, China, e-mail:
[email protected]
ZhongfangTan ZhengzhouUniversity,Zhengzhou,China,e-mail:tzhongfang@
zzu.edu.cn
vii
viii Contributors
Yanping Wang Zhengzhou University, Zhengzhou, China, e-mail: wyp@zzu.
edu.cn
Rina Wu Shenyang Agricultural University, Shenyang, Liaoning, China, e-mail:
[email protected]
Jinzhong Xiao Food Science and Technology Institute, Morinaga Milk Industry
Co. Ltd, Tokyo, Japan, e-mail: [email protected]
Chuncheng Xu China Agriculture University, Beijing, China, e-mail:
[email protected]
Jinsong Yang Hainan University, Haikou, China, e-mail: [email protected]
Zhennai Yang Beijing Technology and Business University, Beijing, China,
e-mail: [email protected]
Jie Yu Key Laboratory of Dairy Biotechnology and Engineering, Ministry of
Education, Inner Mongolia Agricultural University, Hohhot, China, e-mail:
[email protected]
Heping Zhang Key Laboratory of Dairy Biotechnology and Engineering, Min-
istryofEducation,InnerMongoliaAgriculturalUniversity,Hohhot,China,e-mail:
[email protected]
JianguoZhang SouthChinaAgriculturalUniversity,Guangzhou,China,e-mail:
[email protected]
WenyiZhang KeyLaboratoryofDairyBiotechnologyandEngineering,Ministry
of Education, Inner Mongolia Agricultural University, Hohhot, China, e-mail:
[email protected]
Yong Zhang Research Centerfor Nutrition and Food Safety, TheThirdMilitary
Medical University, Chongqing, China, e-mail: [email protected]
Chapter 1
Phylogenesis and Evolution of Lactic Acid
Bacteria
Zhihong Sun, Jie Yu, Tong Dan, Wenyi Zhang and Heping Zhang
Abstract Lactic acid bacteria (LAB) are Gram-positive, usually catalase nega-
tive,microaerophilic,acid-tolerant,non-sporulatingrodsandcoccithatresideina
diversity of different habitats. They are widely used in numerous industrial
applications, ranging from starter cultures in the dairy industry to probiotics in
dietary supplements and bioconversion agents. Despite the functional definition
characterising members of the LAB, they are very heterogeneous from a taxo-
nomic viewpoint.Phylogenetic relationshipsamongstspeciesorsubspeciesinthe
LAB have been hotly disputed. Amongstthe ‘domesticated’ bacteria mostwidely
studiedandexploited,theLABarefoundintwodistinctphyla,namelyFirmicutes
and Actinobacteria. Within the Firmicutes phylum, the most important genera of
LAB are Enterococcus, Lactobacillus, Lactococcus, Leuconostoc, Pediococcus,
StreptococcusandWeissella,whichallbelongtotheorderLactobacillales.Within
the Actinobacteria phylum, LAB belong to the Bifidobacterium genus. In this
chapter,thephylogeneticrelatednessandevolutionaryhistoryofthoseeightmost
important genera of LAB were reviewed.
Z.Sun(&)(cid:1)J.Yu(cid:1)T.Dan(cid:1)W.Zhang(cid:1)H.Zhang
KeyLaboratoryofDairyBiotechnologyandEngineering,MinistryofEducation,
InnerMongoliaAgriculturalUniversity,Hohhot,China
e-mail:[email protected]
J.Yu
e-mail:[email protected]
T.Dan
e-mail:[email protected]
W.Zhang
e-mail:[email protected]
H.Zhang
e-mail:[email protected]
H.ZhangandY.Cai(eds.),LacticAcidBacteria, 1
DOI:10.1007/978-94-017-8841-0_1,
(cid:1)SpringerScience+BusinessMediaDordrecht2014
2 Z.Sunetal.
(cid:1) (cid:1) (cid:1)
Keywords Lactic acid bacteria Taxonomy Phylogenetic relatedness
Evolutionary
1.1 Introduction
Theterm‘lacticacidbacteria’doesnotrelatetoaphylogeneticclassoforganisms,
but rather to the metabolic capabilities of the species whining this group. Lactic
acid bacteria (LAB) are historically defined as a ubiquitous and heterogeneous
family of microbes that can ferment various nutrients into, primarily, lactic acid.
LAB are Gram-positive, usually catalase negative, microaerophilic, acid-tolerant,
non-sporulatingrodsandcoccithatresideinadiversityofdifferenthabitats.These
include human cavities such as the gastrointestinal tract, oral cavity, respiratory
tract and vaginal cavity, as well as a number of environmental niches such as
plants and processed dairy, meat and vegetable products (Klaenhammer et al.
2002, 2005; Kleerebezem and Hugenholtz 2003). LAB are widely used in
numerousindustrialapplications,rangingfromstarterculturesinthedairyindustry
to probiotics in dietary supplements and bioconversion agents. Amongst the
‘domesticated’ bacteria most widely studied and exploited, the LAB are found in
two distinct phyla, namely Firmicutes and Actinobacteria. Within the Firmicutes
phylum, the most important genera of LAB are Enterococcus, Lactobacillus,
Lactococcus, Leuconostoc, Pediococcus, Streptococcus and Weissella, which all
belongtotheorderLactobacillalesandarelow-GCcontentorganisms(31–49%).
Within the Actinobacteria phylum, LAB belong to the Bifidobacterium genus,
which have a high-GC content (58–61 %) (Klaenhammer et al. 2005; Pfeiler and
Klaenhammer 2007; Schleifer and Ludwig 1995a; Horvath et al. 2009).
LAB play an important role in many industrial fermentation processes and
humannutrition.Duetotheirpresenceinthegastrointestinaltract,somemembers
have emerged as probiotics since they are ofhuman origin and conferbenefits on
human health (Klaenhammer et al. 2008; Makarova et al. 2006). Despite the
functional definition characterising members of the LAB, they are very hetero-
geneous from a taxonomic viewpoint (Hammes and Vogel 1995; Zhang et al.
2011;Salvettietal.2013).PhylogeneticrelationshipsamongstspeciesintheLAB
havebeenhotlydisputed.Basedonthephylogeneticrelatednessof16Sribosomal
ribonucleicacid(16SrRNA)sequencesfromdifferentspecies(Woese1987),LAB
have been divided into two major branches, the Clostridium branch and the acti-
nomycetes branch. The typical LAB, such as Lactobacillus, Lactococcus, Leu-
conostoc, Streptococcus, Enterococcus and Pediococcus, belong to the
Clostridium branch. In contrast, the genus Bifidobacterium belongs to the acti-
nomycetes branch (Schleifer and Ludwig 1995a; Stiles and Holzapfel 1997). One
of the foremost debates in LAB phylogeny concerns species in the gener a Lac-
tobacillus, Pediococcus and Leuconostoc, which belong to the families Lacto-
bacillaceae and Leuconostocaceae, these debates have arisen due to severe
disagreements concerning the types of analyses applied to the different available
1 PhylogenesisandEvolutionofLacticAcidBacteria 3
datasets(PfeilerandKlaenhammer2007;Makarovaetal.2006;Collinsetal.1991;
Carretal.2002;Caietal.2009;Claessonetal.2008).Recently,anumberofLAB
genomes have been sequenced and the subsequent explosion of genomic infor-
mation hasfacilitated a better understanding ofLAB characteristics, such astheir
physiology, metabolic capabilities, key gene features and niche adaptation.
Moreover,theavailabilityofgenomesequenceshasprovidedagoodopportunityto
understandLABphylogeneticrelatednessandevolutionaryhistory(Klaenhammer
et al. 2008).
1.2 The Genus Bifidobacterium
1.2.1 History
The first isolation of a Bifidobacterium species was from the faeces of breast-fed
infantsin1899,byHenriTissier,andatthetime,wasdesignatedasBacillusbifidus
(Tissier1899,1900).EventhoughOrla-JensenproposedthegenusBifidobacterium
in1924(leDrORLA-JENSEN1924),thesespeciescontinuedtobeclassifiedinto
other taxonomic groups for several decades; for example Bacillus bifidus, Bacte-
roides bifidus from 1923 to 1934 and Lactobacillus bifidus from 1939 to 1957
(Sgorbatietal.1995;BiavatiandMattarelli1924,2006).Inthe1970s,thesespecies
were reclassified as a separate taxon and designated as the genus Bifidobacterium
comprising11species(Poupardetal.1973;Bergeyetal.1974).Thiswasupdated
to24speciesin1986(Scardovi1986)andthen32speciesand9subspeciesin2012
(Biavati et al. 2012). Currently, there are 41 proposed species and 9 subspecies
(http://www.bacterio.net/bifidobacterium.html, 20 December 2013). These have
been isolated from the gastrointestinal tract (GI) of humans, animals and insects,
and also fromhuman dental caries anddairy products (Table 1.1).
DNA G+C content (mol.%): 46–67.
Type species: Bifidobacterium bifidum (Tissier 1900) Orla-Jensen 1924.
1.2.2 Cell Morphology and Cultural Characteristics
Bifidobacterium species are nonmotile, nonsporeforming, non-gas producing,
Gram-positive, catalase-negative bacteria with a high GC content (46–67 %)
(Biavati and Mattarelli 1924, 2006). Their morphology is generally referred to as
bifid or irregular V- or Y-shaped rods resembling branches. The actual reason for
theirregularshapeofbifidobacteriaisnotyetclearlyunderstood.However,afew
studies have revealed that absence or low concentrations of N-acetylamino sugar
(Glick et al. 1960), Ca2+ions (Kojima et al. 1970) or amino acids (Husain et al.
1972) in the growth media can induce the bifid shape.