Identification of the bacterial biodiversity in koumiss by denaturing gradient gel electrophoresis and species-specific polymerase chain reaction

Bacterial biodiversity in traditional koumiss fermented milk was studied by denaturing gradient gel electrophoresis (DGGE). Target DNA bands were identified according to the reference species ladder, constructed in this study. Comigrating bands present in the DGGE profiles were resolved by species-specific PCR. The results revealed a novel bacterial profile and extensive bacterial biodiversity in koumiss. The dominant lactic acid bacteria included Lactobacillus acidophilus, Lactobacillus helveticus, Lactobacillus fermentum, and Lactobacillus kefiranofaciens. Frequently encountered bacterial species were Enterococcus faecalis, Lactococcus lactis, Lactobacillus paracasei, Lactobacillus kitasatonis, and Lactobacillus kefiri. Leuconostoc mesenteroides, Streptococcus thermophilus, Lactobacillus buchneri, and Lactobacillus jensenii were occasionally found in this product. In addition, L. buchneri, L. jensenii, and L. kitasatonis, which were never previously isolated by culture-dependent methods, were identified for the first time in the Xinjiang koumiss. Furthermore, conventional cultivation was performed by plating samples on M17, de Man-Rogosa-Sharpe, Halligan-Pearce, and Kenner fecal media. The results revealed that lactobacilli were the dominant species in the koumiss ecosystem, which was consistent with the results obtained by the DGGE analysis. This is the first systematic study of the microbial composition in koumiss, and our findings will be helpful in selecting appropriate strains for the manufacture of this product at the industrial level.     

Identification of Lactobacillus from koumiss by conventional and molecular methods

Lactobacilli are considered to be one of the most important potential probiotics in the dairy industry. Twelve strains of Lactobacillus were isolated from home-made koumiss samples, a traditionally fermented mare milk in China. The isolates were identified based on physiological and biochemical characteristics and analysis of 16S RNA sequences. They were proven to be Lactobacillus helveticus, Lactobacillus fermentum, Lactobacillus casei and Lactobacillus plantarum. The results demonstrated that both methods were essential to identify an isolate accurately.     

Diversity of lactic acid bacteria associated with traditional fermented dairy products in Mongolia

Spontaneous milk fermentation has a long history in Mongolia, and beneficial microorganisms have been handed down from one generation to the next for use in fermented dairy products. The objective of this study was to investigate the diversity of lactic acid bacteria (LAB) communities in fermented yak, mare, goat, and cow milk products by analyzing 189 samples collected from 13 different regions in Mongolia. The LAB counts in these samples varied from 3.41 to 9.03 log cfu/mL. Fermented yak and mare milks had almost identical mean numbers of LAB, which were significantly higher than those in fermented goat milk but slightly lower than those in fermented cow milk. In total, 668 isolates were obtained from these samples using de Man, Rogosa, and Sharpe agar and M17 agar. Each isolate was considered to be presumptive LAB based on gram-positive and catalase-negative properties, and was identified at the species level by 16S rRNA gene sequencing, multiplex PCR assay, and restriction fragment length polymorphism analysis. All isolates from Mongolian dairy products were accurately identified as Enterococcus faecalis (1 strain), Enterococcus durans (3 strains), Lactobacillus brevis (3 strains), Lactobacillus buchneri (2 strains), Lactobacillus casei (16 strains), Lactobacillus delbrueckii ssp. bulgaricus (142 strains), Lactobacillus diolivorans (17 strains), Lactobacillus fermentum (42 strains), Lactobacillus helveticus (183 strains), Lactobacillus kefiri (6 strains), Lactobacillus plantarum ssp. plantarum (7 strains), Lactococcus lactis ssp. lactis (7 strains), Leuconostoc lactis (22 strains), Leuconostoc mesenteroides (21 strains), Streptococcus thermophilus (195 strains), and Weissella cibaria (1 strain). The predominant LAB were Strep. thermophilus and Lb. helveticus, which were isolated from all sampling sites. The results demonstrate that traditional fermented dairy products from different regions of Mongolia have complex compositions of LAB species. Such diversity of LAB provides useful information for further studies of probiotic strain selection and starter culture design, with regard to the industrial production of traditional fermented milk.     

Bacterial community succession and metabolite changes during the fermentation of koumiss,a traditional Mongolian fermented beverage

The microbial population in koumiss, a traditional Mongolian fermented beverage, plays a vital role in its nutritional value, beneficial functions, and flavour. We used the Illumina MiSeq platform to investigate the successive bacterial communities produced during koumiss fermentation; dynamic changes in chemical composition of koumiss were also analysed. The correlation between bacterial species and major metabolites was then evaluated. The dominant bacterial species identified during the process of koumiss fermentation were Lactobacillus helveticus, Streptococcus parauberis (phylum Firmicutes), and Acetobacter pasteurianus (phylum Proteobacteria). Lactose content decreased during fermentation, whereas lactic acid, acetic acid, and butyric acid content increased, resulting in decreased pH. The changes in lactose, lactic acid, butyric acid, and pH were mainly correlated with the presence of the bacterial genera Acetobacter, Leuconostoc, Pediococcus, and Bacteroides. Information from these results could advance our understanding of koumiss fermentation, and also help improve the safety, flavour, and therapeutic applications of koumiss.     

Angiotensin I converting enzyme (ACE) inhibitory activity and antihypertensive effect of fermented milk

Milk was fermented with a total of 25 lactic acid bacteria to assay in vitro inhibitory activity towards angiotensin I converting enzyme (ACE). The tested strains belonged to Lactobacillus acidophilus, Lactobacillus casei, Lacobacillus helveticus, Lactobacillus jensenii, Lactobacillus reuteri, Lactobacillus rhamnosus, Lactococcus lactis ssp. lactis, Lactococcus. raffinolactis and Leuconostoc mesenteroides ssp. cremoris. The ACE inhibitory potencies of theses strains varied and seven of them showing the highest ACE inhibitory activity were selected for further studies. The development of ACE inhibitory activity during fermentation correlated with degree of hydrolysis. Modification of fermentation conditions or pH control did not affect the ACE inhibitory activity. ACE inhibitory compounds from Lb. jensenii fermented milk were isolated by reversed phase HPLC and identified by MS-analysis and amino acid sequencing. The active compounds were peptides from β-casein. The milk fermented with Lb. jensenii caused a transient reduction of blood pressure in spontaneously hypertensive rats.     

Identification of Microbial Profile of Koji Using Single Molecule,Real‐Time Sequencing Technology

Koji is a kind of Japanese traditional fermented starter that has been used for centuries. Many fermented foods are made from koji, such as sake, miso, and soy sauce. This study used the single molecule real‐time sequencing technology (SMRT) to investigate the bacterial and fungal microbiota of 3 Japanese koji samples. After SMRT analysis, a total of 39121 high‐quality sequences were generated, including 14354 bacterial and 24767 fungal sequence reads. The high‐quality gene sequences were assigned to 5 bacterial and 2 fungal plyla, dominated by Proteobacteria and Ascomycota, respectively. At the genus level, Ochrobactrum and Wickerhamomyces were the most abundant bacterial and fungal genera, respectively. The predominant bacterial and fungal species were Ochrobactrum lupini and Wickerhamomyces anomalus, respectively. Our study profiled the microbiota composition of 3 Japanese koji samples to the species level precision. The results may be useful for further development of traditional fermented products, especially optimization of koji preparation. Meanwhile, this study has demonstrated that SMRT is a robust tool for analyzing the microbial composition in food samples.     

Effects of applying Lactobacillus helveticus H9 as adjunct starter culture in yogurt fermentation and storage

Lactobacillus helveticus H9 is a probiotic bacterium originating from traditional Tibetan kurut. It has high angiotensin-converting enzyme-inhibitory (ACEI) and antihypertensive activities. We aimed to evaluate the effects of L. helveticus H9 supplementation in yogurt fermentation and storage. We monitored changes of multiple parameters over 28 d of storage at 4°C; namely, pH, titratable acidity, free amino groups, ACEI activity, physical properties, volatile flavor compounds, and sensory quality. Supplementation of L. helveticus H9 enhanced fermented milk acidification and proteolysis, resulting in a shorter fermentation time. The H9 treatment significantly increased the ACEI activity of the fermented milks. Fifteen key volatile flavors were detected by solid-phase microextraction-gas chromatography-mass spectrometry across all samples. More alcohols, aldehydes, and nitrogenous compounds, especially acetoin and benzaldehyde, were detected in the H9-supplemented fermented milks. The human sensory scores for flavor and texture, but not appearance, were lower for the H9-supplemented fermented milks, particularly beyond 2 wk of cold storage. Our results will be of interest to the dairy industry for developing novel functional dairy products.     

基于16S rDNA高通量测序方法比较新疆西北部地区乳品中微生物的多样性

为更加全面地了解新疆特色乳品中微生物多样性,比较不同动物来源的原奶和酸奶的细菌群落结构,运用高通量测序技术,对乳品中细菌16S r DNA V4-V5区测序,进而对新疆克州和塔城地区牛奶、驼奶、马奶、羊奶、酸牛奶、酸驼奶和酸马奶7种乳品中细菌群落组成和多样性进行分析。研究共获得539 557条有效序列,379个OTU。多样性分析表明,原奶样品中细菌Shannon-Wiener指数明显高于酸奶样品。微生物群落组成分析发现,不同乳品之间菌群组成差异较大。7种乳品中的菌群均以厚壁菌门和变形菌门为主,但原奶样品主要以变形菌门为主,而酸奶样品主要以厚壁菌门为主。在属水平上,牛奶主要以假单胞菌属(Pseudomonas)为主,驼奶主要以埃希菌属-志贺菌属(Escherichia-Shigella),马奶主要以明串珠菌属(Leuconostoc)为主,羊奶中的优势菌属为乳球菌属(Lactococcus),而酸牛奶、酸驼奶和酸马奶都是以乳杆菌属(Lactobacillus)为优势菌属。不同动物来源的原奶和酸奶样品中的微生物多样性存在显著差异,并且原奶中检测到的环境污染菌和致病菌(或条件致病菌)的丰度也相对较高。本研究结果将为准确评估乳品中的微生物群落对新疆地区少数民族健康的影响提供一定的数据基础。     

Ribotyping and biotyping of Lactobacillus helveticus from the koumiss

The lactic acid bacteria are very important components involved in the milk products processing. Lactobacillus helveticus, a homofermentative thermophilic lactobacillus commonly occurring in cheeses, has been isolated as the prevailing species in natural koumiss in this work. The species identification of six studied L. helveticus strains was based on rep-PCR fingerprinting with (GTG)₅ primer. Biotyping (API 50CH kit, conventional tests) showed phenotypic heterogeneity among isolates and enabled the identification to the genus Lactobacillus only. Ribotyping with restriction enzyme EcoRI yielded a strain-specific restriction patterns and allowed good strain differentiation. Obtained ribotypes of the isolates originating from the koumiss gave unique band patterns with low similarity to the selected reference cultures of L. helveticus. Despite low number of strains analyzed, the ribotype data showed certain heterogeneity that seemed to be not only strain dependent, but also related to the source of isolates. We concluded that analyzed isolates from koumiss represent a new ecovar, L. helveticus ecovar Koumiss.     

Original features of cell-envelope proteinases of Lactobacillus helveticus. A review

Lactobacillus helveticus is a lactic acid bacterium very used in fermented milks and cheese. The rapid growth of L. helveticus in milk is supported by an efficient cell envelope proteinase (CEP) activity, due to subtilisin-like serine proteases. These enzymes play also crucial roles in texture and flavor formation in dairy products as well as in generating in situ bioactive peptides. In L. helveticus, several genes encoding putative CEPs were detected and characterized by a large intraspecific diversity; little is known about regulation of expression of CEP-encoding genes. Anchored at the bacterial surface, CEPs are large-sized enzymes (> 150 kDa) hydrolyzing β- and α_s1-casein as well. Substrate cleavages occur after almost all types of amino acids residues, but mass spectrometry analysis revealed L. helveticus strains with specific profiles of substrate hydrolysis, which could explain identification of strains associated with interesting technological properties. In this review, the most recent data regarding CEP-encoding genes, CEP activities toward caseins and L. helveticus strain diversity are discussed.     

摩洛哥发酵橄榄汁中乳酸菌的分离鉴定及其多样性研究

为了分离、保藏自然发酵食品中乳酸菌资源,丰富自然发酵食品中乳酸菌多样性信息,本文采用纯培养方法和宏基因组16S rRNA基因测序技术对采集自摩洛哥的2份自然发酵橄榄汁中的乳酸菌进行分离鉴定和多样性研究。结果表明:2份样品中共分离鉴定出52株乳酸菌,分属于3个属、4个种,其中乳酸乳球菌（Lactococcus lactis）为摩洛哥卡萨布兰卡地区发酵橄榄汁中的优势菌种,占总分离株的42.31%,同时还分离到植物乳杆菌和肠球菌;利用PacBio SMRT16S rRNA测序技术,将橄榄汁中的细菌归为5个门、40个属和80个种,优势菌种同样为Lactococcus lactis,其次还检测到干酪乳杆菌（Lactobacillus casei）和植物乳杆菌（Lactobacillus plantarum）。     

Discrimination of dairy industry isolates of the Lactobacillus casei group

Lactobacilli are a major part of the microflora of the gut and of many fermented dairy products, and are found in a variety of environments. Lactobacillus casei, Lactobacillus paracasei, Lactobacillus rhamnosus, and Lactobacillus zeae form a closely related taxonomic group within the facultatively heterofermentative lactobacilli. The classification and nomenclature of these bacteria are controversial. In this study, relationships between these species were investigated using type strains and dairy industry isolates examined with DNA-based techniques and conventional carbohydrate use tests. Carbohydrate use patterns gave poor discrimination of some species, but DNA PCR using specific primers targeted to sequences of the 16S rRNA gene discriminated 4 types consistent with the currently recognized species. Pulsed-field agarose gel electrophoresis of chromosomal NotI restriction fragments identified 18 different band patterns from 21 independent Lactobacillus isolates and confirmed the identity of L. casei strains from 2 culture collections (CSCC 5203 and ASCC 290), both representing the type strain of L. casei. Some isolates were reclassified as L. rhamnosus, suggesting that the prevalence of L. rhamnosus as a natural component of the microflora of dairy foods and dairy environments has previously been underestimated. These methods can provide a practical basis for discrimination of the species and identification of individual industrial strains.     

Invited review: Lactobacillus helveticus—A thermophilic dairy starter related to gut bacteria

The strain Lactobacillus helveticus DPC4571 has emerged as a promising flavor adjunct culture for Cheddar cheese given that it is consistently associated with improved flavor. The availability of the complete genome sequence of Lb. helveticus DPC4571 has enabled the search for the presence or absence of specific genes on the genome, in particular those of technological interest. Indeed, this analysis has facilitated a greater understanding into the functioning of lactic acid bacteria as a whole. The biochemical pathways of Lb. helveticus responsible for producing flavor compounds during cheese ripening are poorly understood but now with the availability of a complete genomic sequence are ripe for exploitation. Bioinformatic analysis of the genome of Lb. helveticus DPC4571 has revealed a plethora of genes with industrial potential including those responsible for key metabolic functions that contribute to cheese flavor development such as proteolysis, lipolysis, and cell lysis. In addition, it has been demonstrated that Lb. helveticus has the potential to produce bioactive peptides such as angiotensin converting enzyme inhibitory activity in fermented dairy products, demonstrating the therapeutic value of this species. A most intriguing feature of the genome of Lb. helveticus DPC4571 is the remarkable similarity in gene content with many intestinal lactobacilli, although originating from considerably different environments. Bioinformatic analysis demonstrated that 65 to 75% of genes were conserved between the commensal and dairy lactobacilli, which allowed key niche-specific gene sets to be described. This review focuses on the isolation, characterization, and exploitation of the Lb. helveticus species with particular emphesis on taking into consideration recent genome sequence data for Lb. helveticus and other Lactobacillus species.     

不同发酵时期酸马奶细菌群落结构

以聚合酶链式反应扩增16S rRNA基因序列采用454焦磷酸测序方法分析酸马奶传统发酵过程中细菌群落结构演替变化。结果表明：在发酵的初期细菌多样性最高,而细菌丰度在72 h时最高;硬壁菌门（Firmicutes）和变形菌门（Proteobacteria）为酸马奶中的优势细菌门;乳杆菌属（Lactobacillus）和乳球菌属（Lactococcus）为其优势细菌属;随着发酵时间的延长,各个细菌门与属都存在上升或下降的趋势变化。本研究可为其他乳制品发酵过程中细菌群落结构研究提供借鉴。     

Effect of using mycotoxin-detoxifying agents in dairy cattle feed on natural whey starter biodiversity

Natural whey cultures (NWC) are undefined multiple-strain bacterial starter communities that can be affected by even small changes along the entire dairy chain. We applied a multidisciplinary approach to investigate how the addition of 2 mycotoxin-detoxifying agents [sodium smectite and lignocellulose-based material (B1); leonardite and betaine (B2)] to cow diets modified the microbiota of the NWC in manufacture of a Grana-like cheese. Microbiological and flow cytometry analyses showed that the content and viability of lactic acid bacteria (LAB) and the total whey microbiota were not affected by the detoxifying agents, and Streptococcus thermophilus, Lactobacillus helveticus, and Limosilactobacillus fermentum were the dominant taxa. Random amplified polymorphic DNA-PCR fingerprinting and metagenomic analysis highlighted differences in the bacterial community of the NWC and in the relative abundance of Bacteroidetes that increased when B1 and B2 were included in the diet. Two of 6 St. thermophilus biotypes were detected only in control samples; conversely, none of the Lb. helveticus biotypes found in control samples were isolated from B1 and B2. In vitro tests showed that the 2 binders did not significantly affect the development of St. thermophilus, but they stimulated the growth of Lb. helveticus strains recovered only from B1 and B2 NWC. The addition of binders in cow feed can affect the LAB biotypes present in NWC.     

Study of bacterial and fungal community structures in traditional koumiss from Inner Mongolia

Koumiss is notable for its nutritional functions, and microorganisms in koumiss determine its versatility. In this study, the bacterial and fungal community structures in traditional koumiss from Inner Mongolia, China, were investigated. Our results demonstrated that 6 bacterial phyla represented by 126 genera and 49 species and 3 fungal phyla represented by 59 genera and 57 species were detected in 11 samples of artisanal koumiss. Among them, Lactobacillus was the predominant genus of bacterium, and Kluyveromyces and Saccharomyces dominated at the fungal genus level. In addition, there were no differences in the bacterial and fungal richness and diversity of koumiss from 3 neighboring administrative divisions in Inner Mongolia, and the bacterial and fungal community structures (the varieties and relative abundance of bacterial and fungal genera and species) were clearly distinct in individual samples. This study provides a comprehensive understanding of the bacterial and fungal population profiles and the predominant genus and species, which would be beneficial for screening, isolation, and culture of potential probiotics to simulate traditional fermentation of koumiss for industrial and standardized production in the future.     

应用Illumina MiSeq测序技术比较传统发酵乳、肉食品中细菌多样性

为全面了解内蒙古特色发酵食品中细菌微生物多样性,比较不同发酵食品的细菌群落结构。运用高通量测序技术,对发酵乳制品(饼状奶酪、棒状奶酪及奶豆腐)和发酵肉制品(发酵香肠、风干羊肉和风干牛肉)中细菌群落组成和多样性进行分析。本研究中共获得194568条有效序列,237个OTU。菌群多样性分析表明:发酵肉制品中菌群Shannon指数较高于发酵乳制品,乳肉制品之间的菌群组成差异较大。发酵乳制品中主要以厚壁菌门为主,而发酵肉制品则以厚壁菌门和变形菌门为主;在属水平上,发酵乳制品的优势菌属为乳杆菌属,而发酵肉制品中的优势菌属为假单胞菌属,次优势菌属为乳杆菌属。在种水平上,由于未检测到的菌群含量较高,所以不能确定乳、肉制品优势菌种,而在发酵乳、肉食品中可检测到的菌群中清酒乳杆菌含量较高。通过16s预测功能分析,发酵乳、肉食品中的绝大部分细菌与转运代谢有关,如脂肪代谢、氨基酸代谢等功能。     

Functional cultures and health benefits

A number of health benefits have been claimed for probiotic bacteria such as Lactobacillus acidophilus, Bifidobacterium spp., and L. casei. These benefits include antimutagenic effects, anticarcinogenic properties, improvement in lactose metabolism, reduction in serum cholesterol, and immune system stimulation. Because of the potential health benefits, these organisms are increasingly being incorporated into dairy foods, particularly yoghurt. In addition to yoghurt, fermented functional foods with health benefits based on bioactive peptides released by probiotic organisms, including Evolus^® and Calpis^®, have been introduced in the market. To maximize effectiveness of bifidus products, prebiotics are used in probiotic foods. Synbiotics are products that contain both prebiotics and probiotics.     

Lactobacillus pentosus dominates spontaneous fermentation of Italian table olives

Culture-dependent and -independent approaches were applied to identify the bacterial species involved in Italian table olive fermentation. Bacterial identification showed that Lactobacillus pentosus was the dominant species although the presence of Lactobacillus plantarum, Lactobacillus casei, Enterococcus durans, Lactobacillus fermentum and Lactobacillus helveticus was observed. Rep-PCR allowed to obtain strain-specific profiles and to establish a correlation with table olive environment. PCR-DGGE (Denaturing Gradient Gel Electrophoresis) confirmed the heterogeneity of bacterial community structure in fermented table olives as well as the prevalence of L. pentosus. The strains were characterized on the basis of technological properties (NaCl tolerance, β-glucosidase activity and the ability to grow in synthetic brine and in presence of 1 g/100 mL oleuropein). L. pentosus showed a high capacity of adaptation to the different conditions characterizing the olive ecosystem. This species showed the highest percentage of strains able to grow in presence of 10 g/100 mL NaCl, oleuropein and in the synthetic brine. Moreover, all the strains belonging to L. pentosus and L. plantarum species showed a β-glucosidase activity. This study allowed both to identify the main species and strains associated to Italian table olives and to obtain a lactic acid bacteria collection to apply as starter culture in the process of olive fermentation.