Intra- and extracellular beta-galactosidases from Bifidobacterium bifidum and B. infantis: molecular cloning, heterologous expression, and comparative characterization

The Genome of Bifidobacterium longum subsp. infantis YLGB-1496 Provides Insights into Its Carbohydrate Utilization and Genetic Stability

Bifidobacterium longum subsp. infantis YLGB-1496 (YLGB-1496) is a probiotic strain isolated from human breast milk. The application of YLGB-1496 is influenced by carbohydrate utilization and genetic stability. This study used genome sequencing and morphology during continuous subculture to determine the carbohydrate utilization characteristics and genetic stability of YLGB-1496. The complete genome sequence of YLGB-1496 consists of 2,758,242 base pairs, 2442 coding sequences, and a GC content of 59.87%. A comparison of carbohydrate transport and metabolism genes of Bifidobacterium longum subsp. infantis (B. infantis) showed that YLGB-1496 was rich in glycosyl hydrolase 13, 20, 25, and 109 gene families. During continuous subculture, the growth characteristics and fermentation activity of the strain were highly stable. The bacterial cell surface and edges of the 1000th-generation strains were progressively smoother and well-defined, with no perforations or breaks in the cell wall. There were 20 SNP loci at the 1000th generation, fulfilling the requirement of belonging to the same strain. The presence of genes associated with cell adhesion and the absence of resistance genes supported the probiotic characteristics of the strain. The data obtained in this study provide insights into broad-spectrum carbohydrate utilization, genomic stability, and probiotic properties of YLGB-1496, which provide theoretical support to promote the use of YLGB-1496.

Linking human milk oligosaccharide metabolism and early life gut microbiota: bifidobacteria and beyond

SUMMARYHuman milk oligosaccharides (HMOs) are complex, multi-functional glycans present in human breast milk. They represent an intricate mix of heterogeneous structures which reach the infant intestine in an intact form as they resist gastrointestinal digestion. Therefore, they confer a multitude of benefits, directly and/or indirectly, to the developing neonate. Certain bifidobacterial species, being among the earliest gut colonizers of breast-fed infants, have an adapted functional capacity to metabolize various HMO structures. This ability is typically observed in infant-associated bifidobacteria, as opposed to bifidobacteria associated with a mature microbiota. In recent years, information has been gleaned regarding how these infant-associated bifidobacteria as well as certain other taxa are able to assimilate HMOs, including the mechanistic strategies enabling their acquisition and consumption. Additionally, complex metabolic interactions occur between microbes facilitated by HMOs, including the utilization of breakdown products released from HMO degradation. Interest in HMO-mediated changes in microbial composition and function has been the focal point of numerous studies, in recent times fueled by the availability of individual biosynthetic HMOs, some of which are now commonly included in infant formula. In this review, we outline the main HMO assimilatory and catabolic strategies employed by infant-associated bifidobacteria, discuss other taxa that exhibit breast milk glycan degradation capacity, and cover HMO-supported cross-feeding interactions and related metabolites that have been described thus far.

Optimization of the production conditions of tri-GOS and lactosucrose from lactose and sucrose with recombinant -galactosidase

Few studies expressed the β-galactosidase encoding gene from L. plantarum in E. coli so far. In the present study, the recombinant β-galactosidase from L. plantarum FMNP01 was used as a catalyst in transgalactosylation to form tri-GOS and lactosucrose. In the presence of lactose and sucrose, six transfer products were formed in the transgalactosylation reaction with recombinant β-galactosidase L.pFMNP01Gal as a catalyst. Three transfer products were tri-galacto-oligosaccharides (tri-GOS), lactosucrose, and lactulose; the other three transfer products needed to be identified further. Based on a single factor test and response surface methodological approach, the optimal transgalactosylation conditions of the production of tri-GOS and lactosucrose were determined as initial sugar concentration of 50%, lactose: sucrose ratio of 1:2, enzyme concentration of 3 U/mL, and reaction time of 6 h at 50 °C resulting in a maximum tri-GOS concentration of 47.69 ± 1.36 g/L and a maximum lactosucrose concentration of 8.18 ± 0.97 g/L.

Untangling human milk oligosaccharides and infant gut microbiome

The developing gut microbiome in infancy plays a key role in shaping the host immune system and metabolic state, and human milk is the main factor influencing its composition. Human milk does not only serve to feed the baby, but also to help the new-born adapt to its new environment and microbial exposures. Human milk protects the infant by providing multiple bioactive molecules, including human milk oligosaccharides (HMOs), which are the third most abundant solid component after lipids and lactose. The infant is unable to digest HMOs, so they reach the small and large intestines intact where they have many roles, including acting as prebiotics. Bifidobacterium spp. are the main, but not the only, commensals equipped with genes for HMO degradation. In this review we will outline the HMOs structures and functions, list the genes needed for their digestion, and describe the main strategies adopted by bacteria for their utilization.

Multitasking in the gut: the X-ray structure of the multidomain BbgIII from Bifidobacterium bifidum offers possible explanations for its alternative functions

β-Galactosidases catalyse the hydrolysis of lactose into galactose and glucose; as an alternative reaction, some β-galactosidases also catalyse the formation of galactooligosaccharides by transglycosylation. Both reactions have industrial importance: lactose hydrolysis is used to produce lactose-free milk, while galactooligosaccharides have been shown to act as prebiotics. For some multi-domain β-galactosidases, the hydrolysis/transglycosylation ratio can be modified by the truncation of carbohydrate-binding modules. Here, an analysis of BbgIII, a multidomain β-galactosidase from Bifidobacterium bifidum, is presented. The X-ray structure has been determined of an intact protein corresponding to a gene construct of eight domains. The use of evolutionary covariance-based predictions made sequence docking in low-resolution areas of the model spectacularly easy, confirming the relevance of this rapidly developing deep-learning-based technique for model building. The structure revealed two alternative orientations of the CBM32 carbohydrate-binding module relative to the GH2 catalytic domain in the six crystallographically independent chains. In one orientation the CBM32 domain covers the entrance to the active site of the enzyme, while in the other orientation the active site is open, suggesting a possible mechanism for switching between the two activities of the enzyme, namely lactose hydrolysis and transgalactosylation. The location of the carbohydrate-binding site of the CBM32 domain on the opposite site of the module to where it comes into contact with the catalytic GH2 domain is consistent with its involvement in adherence to host cells. The role of the CBM32 domain in switching between hydrolysis and transglycosylation modes offers protein-engineering opportunities for selective β-galactosidase modification for industrial purposes in the future.

Improvement in Lactose Tolerance in Hypolactasic Subjects Consuming Ice Creams with High or Low Concentrations of Bifidobacterium bifidum 900791

Although Bifidobacterium bifidum expresses lactase activity, no clinical trials have determined its impact on lactose-intolerant subjects. This study evaluated whether acute and chronic ingestion of ice creams containing B. bifidum 900791 at high (10⁷ CFU/g) or low (10⁵ CFU/g) concentrations improved lactose tolerance in hypolactasic subjects. Fifty subjects were selected based on a positive lactose (20 g) hydrogen breath test (HBT0) and the presence of digestive symptoms. The recruited subjects were required to perform breath tests after the acute ingestion of: (1) ice cream containing 20 g of lactose without a probiotic (HBT1); (2) the same ice cream, accompanied by a lactase tablet (HBT2); (3) the same ice cream containing the low or high dose of probiotic (HBT3-LD and HBT3-HD); and (4) after the chronic consumption of the ice cream without (placebo) or with the low concentration of probiotic for 1 month (HBT4). Significant decreases in H₂ excretion during HBT2 and HBT3-HD as well as digestive symptoms during HBT2, HBT3-HD and HBT3-LD were observed compared to HBT0 and HBT1, while the orocecal transit time increased. Chronic consumption of the probiotic ice cream did not enhance lactose tolerance compared to the placebo. These results suggest that the acute ingestion of ice cream containing high or low concentrations of B. bifidum 900791 improves lactose tolerance in hypolactasic subjects.

Phylogenomic disentangling of the Bifidobacterium longum subsp. infantis taxon

Members of the Bifidobacterium longum species have been shown to possess adaptive abilities to allow colonization of different mammalian hosts, including humans, primates and domesticated mammalian species, such as dogs, horses, cattle and pigs. To date, three subspecies have formally been recognized to belong to this bifidobacterial taxon, i.e. B. longum subsp. longum, B. longum subsp. infantis and B. longum subsp. suis. Although B. longum subsp. longum is widely distributed in the human gut irrespective of host age, B. longum subsp. infantis appears to play a significant role as a prominent member of the gut microbiota of breast-fed infants. Nevertheless, despite the considerable scientific relevance of these taxa and the vast body of genomic data now available, an accurate dissection of the genetic features that comprehensively characterize the B. longum species and its subspecies is still missing. In the current study, we employed 261 publicly available B. longum genome sequences, combined with those of 11 new isolates, to investigate genomic diversity of this taxon through comparative genomic and phylogenomic approaches. These analyses allowed us to highlight a remarkable intra-species genetic and physiological diversity. Notably, characterization of the genome content of members of B. longum subsp. infantis subspecies suggested that this taxon may have acquired genetic features for increased competitiveness in the gut environment of suckling hosts. Furthermore, specific B. longum subsp. infantis genomic features appear to be responsible for enhanced horizontal gene transfer (HGT) occurrences, underpinning an intriguing dedication toward acquisition of foreign DNA by HGT events.

Microbial Glycoside Hydrolases in the First Year of Life: An Analysis Review on Their Presence and Importance in Infant Gut

The first year of life is a crucial period during which the composition and functionality of the gut microbiota develop to stabilize and resemble that of adults. Throughout this process, the gut microbiota has been found to contribute to the maturation of the immune system, in gastrointestinal physiology, in cognitive advancement and in metabolic regulation. Breastfeeding, the “golden standard of infant nutrition,” is a cornerstone during this period, not only for its direct effect but also due to its indirect effect through the modulation of gut microbiota. Human milk is known to contain indigestible carbohydrates, termed human milk oligosaccharides (HMOs), that are utilized by intestinal microorganisms. Bacteria that degrade HMOs like Bifidobacterium longum subsp. infantis, Bifidobacterium bifidum, and Bifidobacterium breve dominate the infant gut microbiota during breastfeeding. A number of carbohydrate active enzymes have been found and identified in the infant gut, thus supporting the hypothesis that these bacteria are able to degrade HMOs. It is suggested that via resource-sharing and cross-feeding, the initial utilization of HMOs drives the interplay within the intestinal microbial communities. This is of pronounced importance since these communities promote healthy development and some of their species also persist in the adult microbiome. The emerging production and accessibility to metagenomic data make it increasingly possible to unravel the metabolic capacity of entire ecosystems. Such insights can increase understanding of how the gut microbiota in infants is assembled and makes it a possible target to support healthy growth. In this manuscript, we discuss the co-occurrence and function of carbohydrate active enzymes relevant to HMO utilization in the first year of life, based on publicly available metagenomic data. We compare the enzyme profiles of breastfed children throughout the first year of life to those of formula-fed infants.

Infant-Associated Bifidobacterial β-Galactosidases and Their Ability to Synthesize Galacto-Oligosaccharides

Galacto-oligosaccharides (GOS) represent non-digestible glycans that are commercially produced by transgalactosylation of lactose, and that are widely used as functional food ingredients in prebiotic formulations, in particular in infant nutrition. GOS consumption has been reported to enhance growth of specific bacteria in the gut, in particular bifidobacteria, thereby supporting a balanced gut microbiota. In a previous study, we assessed the hydrolytic activity and substrate specificity of seventeen predicted β-galactosidases encoded by various species and strains of infant-associated bifidobacteria. In the current study, we further characterized seven out of these seventeen bifidobacterial β-galactosidases in terms of their kinetics, enzyme stability and oligomeric state. Accordingly, we established whether these β-galactosidases are capable of synthesizing GOS via enzymatic transgalactosylation employing lactose as the feed substrate. Our findings show that the seven selected enzymes all possess such transgalactosylation activity, though they appear to differ in their efficiency by which they perform this reaction. From chromatography analysis, it seems that these enzymes generate two distinct GOS mixtures: GOS with a relatively short or long degree of polymerization profile. These findings may be the stepping stone for further studies aimed at synthesizing new GOS variants with novel and/or enhanced prebiotic activities and potential for industrial applications.

Safety and Modulatory Effects of Humanized Galacto-Oligosaccharides on the Gut Microbiome

Complex dietary carbohydrate structures including β(1-4) galacto-oligosaccharides (GOS) are resistant to digestion in the upper gastrointestinal (GI) tract and arrive intact to the colon where they benefit the host by selectively stimulating microbial growth. Studies have reported the beneficial impact of GOS (alone or in combination with other prebiotics) by serving as metabolic substrates for modulating the assembly of the infant gut microbiome while reducing GI infections. N-Acetyl-D-lactosamine (LacNAc, Galβ1,4GlcNAc) is found in breast milk as a free disaccharide. This compound is also found as a component of human milk oligosaccharides (HMOs), which have repeating and variably branched lactose and/or LacNAc units, often attached to sialic acid and fucose monosaccharides. Human glycosyl-hydrolases do not degrade most HMOs, indicating that these structures have evolved as natural prebiotics to drive the proper assembly of the infant healthy gut microbiota. Here, we sought to develop a novel enzymatic method for generating LacNAc-enriched GOS, which we refer to as humanized GOS (hGOS). We showed that the membrane-bound β-hexosyl transferase (rBHT) from Hamamotoa (Sporobolomyces) singularis was able to generate GOS and hGOS from lactose and N-Acetyl-glucosamine (GlcNAc). The enzyme catalyzed the regio-selective, repeated addition of galactose from lactose to GlcNAc forming the β-galactosyl linkage at the 4-position of the GlcNAc and at the 1-position of D-galactose generating, in addition to GOS, LacNAc, and Galactosyl-LacNAc trisaccharides which were produced by two sequential transgalactosylations. Humanized GOS is chemically distinct from HMOs, and its effects in vivo have yet to be determined. Thus, we evaluated its safety and demonstrated the prebiotic's ability to modulate the gut microbiome in 6-week-old C57BL/6J mice. Longitudinal analysis of gut microbiome composition of stool samples collected from mice fed a diet containing hGOS for 5 weeks showed a transient reduction in alpha diversity. Differences in microbiome community composition mostly within the Firmicutes phylum were observed between hGOS and GOS, compared to control-fed animals. In sum, our study demonstrated the biological synthesis of hGOS, and signaled its safety and ability to modulate the gut microbiome in vivo, promoting the growth of beneficial microorganisms, including Bifidobacterium and Akkermansia.

Crude Pectic Oligosaccharide Recovery from Thai Chok Anan Mango Peel Using Pectinolytic Enzyme Hydrolysis

Pectin recovered from mango peel biomass can be used as a potential source for pectic oligosaccharide hydrolysate with excellent probiotic growth-enhancing performance and prebiotic potentials. Consequently, the objectives of the current study were to optimise the enzyme hydrolysis treatment of mango peel pectin (MPP) and to evaluate the pectic oligosaccharide effects of Lactobacillus reuteri DSM 17938 and Bifidobacterium animalis TISTR 2195. Mango of "chok anan" variety was chosen due to its excessive volume of biomass in processing and high pectin content. The optimal treatment for mango peel pectic oligosaccharide (MPOS) valorisation was 24 h of fermentation with 0.3% (v/v) pectinase. This condition provided small oligosaccharides with the molecular weight of 643 Da that demonstrated the highest score of prebiotic activity for both of B. animalis TISTR 2195 (7.76) and L. reuteri DSM 17938 (6.87). The major sugar compositions of the oligosaccharide were fructose (24.41% (w/w)) and glucose (19.52% (w/w)). For the simulation of prebiotic fermentation, B. animalis TISTR 2195 showed higher proliferation in 4% (w/v) of MPOS supplemented (8.92 log CFU/mL) than that of L. reuteri (8.53 CFU/mL) at 72 h of the fermentation time. The main short chain fatty acids (SCFAs) derived from MPOS were acetic acid and propionic acid. The highest value of total SCFA was achieved from the 4% (w/v) MPOS supplementation for both of B. animalis (68.57 mM) and L. reuteri (69.15 mM). The result of this study therefore conclusively advises that MPOS is a novel pectic oligosaccharide resource providing the opportunity for the sustainable development approach through utilising by-products from the fruit industry.

β-Galactosidase: From its source and applications to its recombinant form

Carbohydrate-active enzymes are a group of important enzymes playing a critical role in the degradation and synthesis of carbohydrates. Glycosidases can hydrolyze glycosides into oligosaccharides, polysaccharides, and glycoconjugates via a cost-effective approach. Lactase is an important member of β-glycosidases found in higher plants, animals, and microorganisms. β-Galactosidases can be used to degrade the milk lactose for making lactose-free milk, which is sweeter than regular milk and is suitable for lactose-intolerant people. β-Galactosidase is employed by many food industries to degrade lactose and improve the digestibility, sweetness, solubility, and flavor of dairy products. β-Galactosidase enzymes have various families and are applied in the food-processing industries such as hydrolyzed-milk products, whey, and galactooligosaccharides. Thus, this enzyme is a valuable protein which is now produced by recombinant technology. In this review, origins, structure, recombinant production, and critical modifications of β-galactosidase for improving the production process are discussed. Since β-galactosidase is a valuable enzyme in industry and health care, a study of its various aspects is important in industrial biotechnology and applied biochemistry.

Arabinogalactan Utilization by Bifidobacterium longum subsp. longum NCC 2705 and Bacteroides caccae ATCC 43185 in Monoculture and Coculture

Arabinogalactan (AG) has been studied as a potential prebiotic in view of stimulating bifidobacteria presence in the gut microbiota. However, bifidobacteria prefer fermentation of oligosaccharides to that of polysaccharides. The contribution of other gut bacteria may allow better growth of bifidobacteria on AG. β-galactanases and β-galactosidases are the main enzymes for the degradation of AG. Additional enzymes such as α-L-arabinofuranosidase and β-L-arabinopyranosidase are required to remove the arabinose side chains. All of these predicted functions are encoded by the genomes of both Bifidobacterium longum subsp. longum NCC 2705 and Bacteroides caccae ATCC 43185. However, neither strain was able to grow significantly on AG, with 25% (B. longum subsp. longum NCC 2705) and 39% (Bac. caccae ATCC 43185) of AG degraded after 48-h fermentation, respectively. In this study, the β-galactanase, β-galactosidase, α-L-arabinofuranosidase, and β-L-arabinopyranosidase from both strains were investigated. The extracellular β-galactosidases of both B. longum subsp. longum NCC 2705 and Bac. caccae ATCC 43185 were able to cleave the β-1,3; 1,4 and 1,6 linkages. However, the β-galactosidase activity of B. longum subsp. longum NCC 2705 was weaker for the β-1,4 linkage, compared with the β-1,3 and 1,6 linkages. The arabinose side chains of AG inhibited the cleavage of β-1,3 and 1,6 linkages by the endo-β-galactanase from both strains, and partially inhibited the cleavage of β-1,4 linkages by the endo-β-1,4 galactanase from Bac. caccae ATCC 43185. The α-L-arabinofuranosidase and β-L-arabinopyranosidase from both strains were unable to cleave arabinose from AG under the conditions used. These results show limited breakdown of AG by these two strains in monoculture. When cocultured with Bac. caccae ATCC 43185, B. longum subsp. longum NCC 2705 grew significantly better than in monoculture on AG after 6 h of fermentation (p < 0.05). The coculture showed 48% AG degradation after 48 h of fermentation, along with reduced pH. Furthermore, compared to monoculture of Bac. caccae ATCC 43185, the concentration of succinate significantly increased from 0.01 ± 0.01 to 4.41 ± 0.61 mM, whereas propionate significantly decreased from 13.07 ± 0.37 to 9.75 ± 2.01 mM in the coculture (p < 0.05). These results suggest that the growth and metabolic activities of Bac. caccae ATCC 43185 were restrained in the coculture, as the pH decreased due to the metabolism of B. longum subsp. longum NCC 2705.

Hydrolysis of Lactose and Transglycosylation of Selected Sugar Alcohols by LacA β-Galactosidase from Lactobacillus plantarum WCFS1

The production, biochemical characterization, and carbohydrate specificity of LacA β-galactosidase (locus lp_3469) belonging to the glycoside hydrolase family 42 from the probiotic organism Lactobacillus plantarum WCFS1 are addressed. The β-d-galactosidase activity was maximal in the pH range of 4.0-7.0 and at 30-37 °C. High hydrolysis capacity toward the β(1 → 4) linkages between galactose and glucose (lactose) or fructose (lactulose) was found. High efficiency toward galactosyl derivative formation was observed when lactose and glycerol, xylitol, or erythritol were used. Galactosyl derivatives of xylitol were characterized for the first time as 3-O-β-d-galactopyranosyl-xylitol and 1-O-β-d-galactopyranosyl-xylitol, displaying high preference of LacA β-galactosidase for the transfer of galactosyl residues from lactose to the C1 or C3 hydroxyl group of xylitol. These results indicate the feasibility of using LacA β-galactosidase for the synthesis of different galactosyl-polyols, which could be promising candidates for beneficial and appealing functional and technological applications such as novel prebiotics or hypocaloric sweeteners.

Metabolism of the predominant human milk oligosaccharide fucosyllactose by an infant gut commensal

A number of bifidobacterial species are found at a particularly high prevalence and abundance in faecal samples of healthy breastfed infants, a phenomenon that is believed to be, at least partially, due to the ability of bifidobacteria to metabolize Human Milk Oligosaccharides (HMOs). In the current study, we isolated a novel strain of Bifidobacterium kashiwanohense, named APCKJ1, from the faeces of a four-week old breastfed infant, based on the ability of the strain to utilise the HMO component fucosyllactose. We then determined the full genome sequence of this strain, and employed the generated data to analyze fucosyllactose metabolism in B. kashiwanohense APCKJ1. Transcriptomic and growth analyses, combined with metabolite analysis, in vitro hydrolysis assays and heterologous expression, allowed us to elucidate the pathway for fucosyllactose metabolism in B. kashiwanohense APCKJ1. Homologs of the key genes for this metabolic pathway were identified in particular in infant-derived members of the Bifdobacterium genus, revealing the apparent niche-specific nature of this pathway, and allowing a broad perspective on bifidobacterial fucosyllactose and L-fucose metabolism.

A New β-Galactosidase from the Antarctic Bacterium Alteromonas sp. ANT48 and Its Potential in Formation of Prebiotic Galacto-Oligosaccharides

As an important medical enzyme, β-galactosidases catalyze transgalactosylation to form prebiotic Galacto-Oligosaccharides (GOS) that assist in improving the effect of intestinal flora on human health. In this study, a new glycoside hydrolase family 2 (GH2) β-galactosidase-encoding gene, galA, was cloned from the Antarctic bacterium Alteromonas sp. ANT48 and expressed in Escherichia coli. The recombinant β-galactosidase GalA was optimal at pH 7.0 and stable at pH 6.6–7.0, which are conditions suitable for the dairy environment. Meanwhile, GalA showed most activity at 50 °C and retained more than 80% of its initial activity below 40 °C, which makes this enzyme stable in normal conditions. Molecular docking with lactose suggested that GalA could efficiently recognize and catalyze lactose substrates. Furthermore, GalA efficiently catalyzed lactose degradation and transgalactosylation of GOS in milk. A total of 90.6% of the lactose in milk could be hydrolyzed within 15 min at 40 °C, and the GOS yield reached 30.9%. These properties make GalA a good candidate for further applications.

Characterization of GH2 and GH42 β-galactosidases derived from bifidobacterial infant isolates

Bifidobacteria are among the first and most abundant bacterial colonizers of the gastrointestinal tract of (breast-fed) healthy infants. Their success of colonising the infant gut is believed to be, at least partly, due to their ability to metabolize available carbon sources by means of secreted or intracellular glycosyl hydrolases (GHs). Among these, β-galactosidases are particularly relevant as they allow bifidobacteria to grow on β-galactosyl-linked saccharidic substrates, which are present in copious amounts in the milk-based diet of their infant host (e.g. lactose and human milk oligosaccharides). In the present study we employed an in silico analysis to identify GH family 2 and 42 β-galactosidases encoded by typical infant-associated bifidobacteria. Comparative genome analysis followed by characterisation of selected β-galactosidases revealed how these GH2 and GH42 members are distributed among these infant-associated bifidobacteria, while their hydrolytic activity towards growth substrates commonly available in the infant gut were also assessed.

Bifidobacterium breve UCC2003 Employs Multiple Transcriptional Regulators To Control Metabolism of Particular Human Milk Oligosaccharides

Bifidobacterial carbohydrate metabolism has been studied in considerable detail for a variety of both plant- and human-derived glycans, particularly involving the bifidobacterial prototype strain Bifidobacterium breve UCC2003. We recently elucidated the metabolic pathways by which the human milk oligosaccharide (HMO) constituents lacto-N-tetraose (LNT), lacto-N-neotetraose (LNnT) and lacto-N-biose (LNB) are utilized by B. breve UCC2003. However, to date, no work has been carried out on the regulatory mechanisms that control the expression of the genetic loci involved in these HMO metabolic pathways. In this study, we describe the characterization of three transcriptional regulators and the corresponding operator and associated (inducible) promoter sequences, with the latter governing the transcription of the genetic elements involved in LN(n)T/LNB metabolism. The activity of these regulators is dependent on the release of specific monosaccharides, which are believed to act as allosteric effectors and which are derived from the corresponding HMOs targeted by the particular locus.IMPORTANCE Human milk oligosaccharides (HMOs) are a key factor in the development of the breastfed-infant microbiota. They function as prebiotics, selecting for a specific range of microbes, including a number of infant-associated species of bifidobacteria, which are thought to provide a range of health benefits to the infant host. While much research has been carried out on elucidating the mechanisms of HMO metabolism in infant-associated bifidobacteria, to date there is very little understanding of the transcriptional regulation of these pathways. This study reveals a multicomponent transcriptional regulation system that controls the recently identified pathways of HMO metabolism in the infant-associated Bifidobacterium breve prototype strain UCC2003. This not only provides insight into the regulatory mechanisms present in other infant-associated bifidobacteria but also provides an example of a network of sequential steps regulating microbial carbohydrate metabolism.

β- ГАЛАКТОЗИДАЗНА АКТИВНІСТЬ БАКТЕРІЙ, ЯК КРИТЕРІЙ ВІДБОРУ ШТАМІВ ДО СКЛАДУ БАКТЕРІАЛЬНИХ ПРЕПАРАТІВ

β-галактозидазна активність є одним з критеріїв відбору штамів до складу бактеріальних препаратів для кисломолочних продуктів спеціального призначення. Саме цей фермент є ключовим у розщепленні лактози молока мікроорганізмами закваски. Одним з важливих критеріїв для складання заквашувальних композицій у виробництві кисломолочних продуктів є їхній склад.У роботі охарактеризовані основні етапи підбору культур лакто-, біфідо- та пропіоновокислих бактерій та створення на їх основі композицій з високою β-галактозидазної активністю для виробництва ферментованих молочних продуктів. Встановлено, що результатом розвитку штамів термофільних стрептококові у молоці є максимальне зниження вмісту лактози , це свідчить про їх високу здатність до продукування β-галактозидази порівнянно з Bifidobacterium ssp та Propionibacterium freudenreichii ssp. schermanii. Найбільшу β-галактозидазну активність проявляє симбіоз мікроорганізмів, що складається з термофільних стрептококів, біфідобактерій та пропіоновокислих бактеріц, а саме – 604 А/хв .Як відомо, якість та біологічна цінність кисломолочних продуктів напряму залежать від застосованих заквашувальних препаратів. Тому, з метою отримання кисломолочного продукту спеціального призначення з низькою концентрацією лактози, було досліджено високоактивні штами мікроорганізмів. Утилізація лактози в готовому продукті для досліджених штамів та їх комбінацій варіює в межах від 12,1 % до 35,8 % від початкової її концентрації. Показано, що β-галактозидазна активність та утилізація лактози в готовому продукті є штамоспецифічними ознакамиЗа результатами проведених досліджень для виробництва кисломолочного продукту спеціального призначення рекомендовано використання композиції на основі штамів Streptococcus thermophilus, Bifidobacterium bifidum, B. longum B. adolescentis та Propionibacterium freudenreichii ssp. schermanii, що входять до складу бактеріального препарату.

Bifidobacterium breve UCC2003 metabolises the human milk oligosaccharides lacto-N-tetraose and lacto-N-neo-tetraose through overlapping, yet distinct pathways

In this study, we demonstrate that the prototype B. breve strain UCC2003 possesses specific metabolic pathways for the utilisation of lacto-N-tetraose (LNT) and lacto-N-neotetraose (LNnT), which represent the central moieties of Type I and Type II human milk oligosaccharides (HMOs), respectively. Using a combination of experimental approaches, the enzymatic machinery involved in the metabolism of LNT and LNnT was identified and characterised. Homologs of the key genetic loci involved in the utilisation of these HMO substrates were identified in B. breve, B. bifidum, B. longum subsp. infantis and B. longum subsp. longum using bioinformatic analyses, and were shown to be variably present among other members of the Bifidobacterium genus, with a distinct pattern of conservation among human-associated bifidobacterial species.

Two β-galactosidases from the human isolate Bifidobacterium breve DSM 20213: molecular cloning and expression, biochemical characterization and synthesis of galacto-oligosaccharides

Two β-galactosidases, β-gal I and β-gal II, from Bifidobacterium breve DSM 20213, which was isolated from the intestine of an infant, were overexpressed in Escherichia coli with co-expression of the chaperones GroEL/GroES, purified to electrophoretic homogeneity and biochemically characterized. Both β-gal I and β-gal II belong to glycoside hydrolase family 2 and are homodimers with native molecular masses of 220 and 211 kDa, respectively. The optimum pH and temperature for hydrolysis of the two substrates o-nitrophenyl-β-D-galactopyranoside (oNPG) and lactose were determined at pH 7.0 and 50°C for β-gal I, and at pH 6.5 and 55°C for β-gal II, respectively. The kcat/Km values for oNPG and lactose hydrolysis are 722 and 7.4 mM-1s-1 for β-gal I, and 543 and 25 mM-1s-1 for β-gal II. Both β-gal I and β-gal II are only moderately inhibited by their reaction products D-galactose and D-glucose. Both enzymes were found to be very well suited for the production of galacto-oligosaccharides with total GOS yields of 33% and 44% of total sugars obtained with β-gal I and β-gal II, respectively. The predominant transgalactosylation products are β-D-Galp-(1→6)-D-Glc (allolactose) and β-D-Galp-(1→3)-D-Lac, accounting together for more than 75% and 65% of the GOS formed by transgalactosylation by β-gal I and β-gal II, respectively, indicating that both enzymes have a propensity to synthesize β-(1→6) and β-(1→3)-linked GOS. The resulting GOS mixtures contained relatively high fractions of allolactose, which results from the fact that glucose is a far better acceptor for galactosyl transfer than galactose and lactose, and intramolecular transgalactosylation contributes significantly to the formation of this disaccharide.

Comparison of chemical washing and physical cell-disruption approaches to assess the surface adsorption and internalization of cadmium by Cupriavidus metallidurans CH34

Bacterial biosorption of heavy metals is often considered as a surface complexation process, without considering other retention compartments than cell walls. Although this approach gives a good description of the global biosorption process, it hardly permits the prediction of the fate of biosorbed metals in the environment. This study examines the subcellular distribution of cadmium (Cd) in the metal-tolerant bacterium Cupriavidus metallidurans CH34 through the comparison of an indirect chemical method (washing cells with EDTA) and a direct physical method (physical disruption of cells). The chemical washing approach presented strong experimental biases leading to the overestimation of washed amount of Cd, supposedly bound to cell membranes. On the contrary, the physical disruption approach gave reproducible and robust results of Cd subcellular distribution. Unexpectedly, these results showed that over 80% of passively biosorbed Cd is internalized in the cytoplasm. In disagreement with the common concept of surface complexation of metals onto bacteria the cell wall was poorly reactive to Cd. Our results indicate that metal sorption onto bacterial surfaces is only a first step in metal management by bacteria and open new perspectives on metal biosorption by bacteria in the environment, with implications for soil bioremediation or facilitated transport of metals by bacteria.

Metabolism of isomalto-oligosaccharides by Lactobacillus reuteri and bifidobacteria

Commercial isomalto-oligosaccharides (IMO) are functional food ingredients. They are composed of α(1→6)- and α(1→4)-linked oligosaccharides. IMO are partially indigestible, and dietary IMO stimulate beneficial members of intestinal microbiota, including lactobacilli and bifidobacteria. However, data on IMO metabolism by lactobacilli are not available. It was the aim of this study to identify metabolic pathways of IMO metabolism in lactobacilli. This study focused on the host-adapted species Lactobacillus reuteri. Metabolism of bifidobacteria was analysed for comparison. Commercial IMO contained IMO with a degree of polymerization (DP) of up to four and panose-series oligosaccharides (POS) with a DP of up to 5. Lactobacilli metabolized isomaltose preferentially over oligosaccharides with higher DP. Bifidobacteria preferentially metabolized oligosaccharides with higher DP and accumulated glucose. Metabolism of IMO and POS by L. reuteri was attributed to α(1→6)-specific glucanase DexB and maltose phosphorylase. Contribution of maltose phosphorylase was verified by quantification of IMO and POS phosphorolysis in crude cellular extracts of L. reuteri 100-23. In conclusion, metabolism of IMO by lactobacilli is limited to short-chain oligosaccharides, while bifidobacteria preferentially metabolize oligosaccharides with higher DP. The functionality of commercial IMO can thus be modified by degree of polymerization.

SIGNIFICANCE AND IMPACT OF THE STUDY

Isomalto-oligosaccharides (IMO) are applied as functional food ingredients, but the composition and biological functionality of current commercial products are poorly documented. This study is the first to analyse IMO metabolism by Lactobacillus reuteri. Bifidobacteria were used for comparison. Commercial IMO contained IMO with degree of polymerization (DP) of up to four and panose-series oligosaccharides with DP of up to 5. L. reuteri preferentially metabolized short-chain oligosaccharides, whereas bifidobacteria preferentially metabolized higher oligosaccharides. Results of this study allow the modification of the biological and technological functionality of commercial IMO by adjustment of the degree of polymerization and will thus facilitate the application development for IMO.

Transcriptional and functional characterization of genetic elements involved in galacto-oligosaccharide utilization by Bifidobacterium breve UCC2003

Several prebiotics, such as inulin, fructo-oligosaccharides and galacto-oligosaccharides, are widely used commercially in foods and there is convincing evidence, in particular for galacto-oligosaccharides, that prebiotics can modulate the microbiota and promote bifidobacterial growth in the intestinal tract of infants and adults. In this study we describe the identification and functional characterization of the genetic loci responsible for the transport and metabolism of purified galacto-oligosaccharides (PGOS) by Bifidobacterium breve UCC2003. We further demonstrate that an extracellular endogalactanase specified by several B. breve strains, including B. breve UCC2003, is essential for partial degradation of PGOS components with a high degree of polymerization. These partially hydrolysed PGOS components are presumed to be transported into the bifidobacterial cell via various ABC transport systems and sugar permeases where they are further degraded to galactose and glucose monomers that feed into the bifid shunt. This work significantly advances our molecular understanding of bifidobacterial PGOS metabolism and its associated genetic machinery to utilize this prebiotic.

Hydrogen cyanide synthesis and antifungal activity of the biocontrol strain Pseudomonas fluorescens In5 from Greenland is highly dependent on growth medium

Hydrogen cyanide (HCN) is a secondary metabolite produced by many antagonistic Pseudomonas species. In the present study, the gene cluster encoding HCN synthesis in a newly isolated Pseudomonas fluorescens strain, In5, from South Greenland was investigated. Sequence analysis showed that the Greenlandic hcn gene cluster comprises a novel hcn cluster. Transposon mutagenesis of strain In5 resulted in mutants In5-2E1 and In5-1H7 with no production of HCN, and mutant In5-6B9 with reduced HCN synthesis. In mutant In5-2E1, the transposon was inserted into the hcnC gene; in mutant In5-1H7, the Tn5 insertion was found in a region upstream of a putative malate:quinone oxidoreductase gene (mqo); and in mutant In5-6B9, the transposon disrupted a probable enoyl-CoA hydratase/isomerase gene. In vitro inhibition experiments with In5 (wild type) and In5-2E1 (mutant) showed that in nitrogen-rich Luria-Bertani medium, strain In5 but not the hcn mutant In5-2E1 produced HCN and inhibited the growth of hyphae of Rhizoctonia solani and Pythium aphanidermatum . In contrast, when cultivating the strains in the carbohydrate-rich potato dextrose medium, neither of the strains produced any HCN, and thus, they were unable to inhibit hyphal growth of fungi. These experiments strongly indicate that the synthesis of HCN is highly dependent on the growth medium used.

A selected probiotic strain of Lactobacillus fermentum CM33 isolated from breast-fed infants as a potential source of β-galactosidase for prebiotic oligosaccharide synthesis

Lactic acid bacteria from healthy breast-fed infants were isolated and screened for β-galactosidase production in MRS broth. Among 49 isolates that exhibited the yellow clear zone on MRS agar supplemented with bromocresol blue, the isolate CM33 was selected as being the highest β-galactosidase producer and was identified as Lactobacillus fermentum based on its morphological characteristics and 16S rDNA nucleotide sequence. L. fermentum CM33 exhibited a good survival rate under the simulated stomach passage model, comparable to known probiotic strains L. gallinarum JCM2011 and L. agilis JCM1187. L. fermentum CM33 was antagonistic to pathogenic bacteria Listeria monocytogenes, Escherichia coli 0157:H7, Salmonella typhi, and Salmonella enteriditis, using the well diffusion method. In addition, the selected lactobacilli exhibited a high growth rate when cultivated in modified MRS containing commercial galactooligosaccharide (GOS) as a sole carbon source, as well as in glucose. A preliminary study on the enzymatic synthesis of oligosaccharide using crude β-galactosidase revealed the capability for oligosaccharide synthesis by the transgalactosylation activity.

Hierarchical classification of glycoside hydrolases

This review deals with structural and functional features of glycoside hydrolases, a widespread group of enzymes present in almost all living organisms. Their catalytic domains are grouped into 120 amino acid sequence-based families in the international classification of the carbohydrate-active enzymes (CAZy database). At a higher hierarchical level some of these families are combined in 14 clans. Enzymes of the same clan have common evolutionary origin of their genes and share the most important functional characteristics such as composition of the active center, anomeric configuration of cleaved glycosidic bonds, and molecular mechanism of the catalyzed reaction (either inverting, or retaining). There are now extensive data in the literature concerning the relationship between glycoside hydrolase families belonging to different clans and/or included in none of them, as well as information on phylogenetic protein relationship within particular families. Summarizing these data allows us to propose a multilevel hierarchical classification of glycoside hydrolases and their homologs. It is shown that almost the whole variety of the enzyme catalytic domains can be brought into six main folds, large groups of proteins having the same three-dimensional structure and the supposed common evolutionary origin.

Bifidobacterium longum subsp. infantis uses two different β-galactosidases for selectively degrading type-1 and type-2 human milk oligosaccharides

The breast-fed infant intestine is often colonized by particular bifidobacteria, and human milk oligosaccharides (HMOs) are considered to be bifidogenic. Recent studies showed that Bifidobacterium longum subsp. infantis can grow on HMOs as the sole carbon source. This ability has been ascribed to the presence of a gene cluster (HMO cluster-1) contained in its genome. However, the metabolism of HMOs by the organism remains unresolved because no enzymatic studies have been completed. In the present study, we characterized β-galactosidases of this subspecies to understand how the organism degrades type-1 (Galβ1-3GlcNAc) and type-2 (Galβ1-4GlcNAc) isomers of HMOs. The results revealed that the locus tag Blon_2016 gene, which is distantly located from the HMO cluster-1, encodes a novel β-galactosidase (Bga42A) with a significantly higher specificity for lacto-N-tetraose (LNT; Galβ1-3GlcNAcβ1-3Galβ1-4Glc) than for lacto-N-biose I (Galβ1-3GlcNAc), lactose (Lac) and type-2 HMOs. The proposed name of Bga42A is LNT β-1,3-galactosidase. The Blon_2334 gene (Bga2A) located within the HMO cluster-1 encodes a β-galactosidase specific for Lac and type-2 HMOs. Real-time quantitative reverse transcription-polymerase chain reaction analysis revealed the physiological significance of Bga42A and Bga2A in HMO metabolism. The organism therefore uses two different β-galactosidases to selectively degrade type-1 and type-2 HMOs. Despite the quite rare occurrence in nature of β-galactosidases acting on type-1 chains, the close homologs of Bga42A were present in the genomes of infant-gut associated bifidobacteria that are known to consume LNT. The predominance of type-1 chains in HMOs and the conservation of Bga42A homologs suggest the coevolution of these bifidobacteria with humans.

Carbohydrate metabolism in Bifidobacteria

Members of the genus Bifidobacterium can be found as components of the gastrointestinal microbiota, and are believed to play an important role in maintaining and promoting human health by eliciting a number of beneficial properties. Bifidobacteria can utilize a diverse range of dietary carbohydrates that escape degradation in the upper parts of the intestine, many of which are plant-derived oligo- and polysaccharides. The gene content of a bifidobacterial genome reflects this apparent metabolic adaptation to a complex carbohydrate-rich gastrointestinal tract environment as it encodes a large number of predicted carbohydrate-modifying enzymes. Different bifidobacterial strains may possess different carbohydrate utilizing abilities, as established by a number of studies reviewed here. Carbohydrate-degrading activities described for bifidobacteria and their relevance to the deliberate enhancement of number and/or activity of bifidobacteria in the gut are also discussed in this review.

Beta-galactosidase from Lactobacillus pentosus: purification, characterization and formation of galacto-oligosaccharides

A novel heterodimeric beta-galactosidase with a molecular mass of 105 kDa was purified from crude cell extracts of the soil isolate Lactobacillus pentosus KUB-ST10-1 using ammonium sulphate fractionation followed by hydrophobic interaction and affinity chromatography. The electrophoretically homogenous enzyme has a specific activity of 97 U(oNPG)/mg protein. The K(m), k(cat) and k(cat)/K(m) values for lactose and o-nitrophenyl-beta-D-galactopyranoside (oNPG) were 38 mM, 20 s(-1), 530 M(-1).s(-1) and 1.67 mM, 540 s(-1), 325 000 M(-1).s(-1), respectively. The temperature optimum of beta-galactosidase activity was 60-65 degrees C for a 10-min assay, which is considerably higher than the values reported for other lactobacillal beta-galactosidases. Mg(2+) ions enhanced both activity and stability significantly. L. pentosus beta-galactosidase was used for the production of prebiotic galacto-oligosaccharides (GOS) from lactose. A maximum yield of 31% GOS of total sugars was obtained at 78% lactose conversion. The enzyme showed a strong preference for the formation of beta-(1-->3) and beta-(1-->6) linkages, and the main transgalactosylation products identified were the disaccharides beta-D-Galp-(1-->6)-D-Glc, beta-D-Galp-(1-->3)-D-Glc, beta-D-Galp-(1-->6)-D-Gal, beta-D-Galp-(1-->3)-D-Gal, and the trisaccharides beta-D-Galp-(1-->3)-D-Lac, beta-D-Galp-(1-->6)-D-Lac.

Identification, cloning and expression of a cold-active beta-galactosidase from a novel Arctic bacterium, Alkalilactibacillus ikkense

A novel, cold-active beta-galactosidase was isolated from an Arctic Gram-positive bacterium, Alkalilactibacillus ikkense. The corresponding gene was cloned and expressed as an active enzyme in Escherichia coli. Denaturing gel electrophoresis of both the native and the recombinant beta-galactosidase showed a monomeric molecular weight of 115-120 kDa. Analysis of the DNA sequence showed sequence similarity to known Glycosyl Hydrolase Family 2 beta-galactosidases from the genera Bacillus, Paenibacillus, Geobacillus, and Lactobacillus. The beta-galactosidase from this study was purified and shown to be highly active at low temperatures with more than 60% of its maximal activity maintained at 0 degrees C. The apparent optimal activity was observed at temperatures between 20 degrees C and 30 degrees C and at pH 8. The purified recombinant enzyme was stable without stabilizing agents for more than 100 hours at temperatures at and below 10 degrees C. At temperatures 40 degrees C and above, the beta-galactosidase was irreversibly inactivated within 10 minutes. When lactose was present in substantial amounts, the enzyme displayed transgalactosylation activity. Comparison of the beta-galactosidase with a commercially available enzyme showed that the conversion rate of the A. ikkense enzyme was approximately two-fold higher at temperatures between 0 degrees C and 20 degrees C.

Characterization of novel beta-galactosidase activity that contributes to glycoprotein degradation and virulence in Streptococcus pneumoniae

The pneumococcus obtains its energy from the metabolism of host glycosides. Therefore, efficient degradation of host glycoproteins is integral to pneumococcal virulence. In search of novel pneumococcal glycosidases, we characterized the Streptococcus pneumoniae strain D39 protein encoded by SPD_0065 and found that this gene encodes a beta-galactosidase. The SPD_0065 recombinant protein released galactose from desialylated fetuin, which was used here as a model of glycoproteins found in vivo. A pneumococcal mutant with a mutation in SPD_0065 showed diminished beta-galactosidase activity, exhibited an extended lag period in mucin-containing defined medium, and cleaved significantly less galactose than the parental strain during growth on mucin. As pneumococcal beta-galactosidase activity had been previously attributed solely to SPD_0562 (bgaA), we evaluated the contribution of SPD_0065 and SPD_0562 to total beta-galactosidase activity. Mutation of either gene significantly reduced enzymatic activity, but beta-galactosidase activity in the double mutant, although significantly less than that in either of the single mutants, was not completely abolished. The expression of SPD_0065 in S. pneumoniae grown in mucin-containing medium or tissues harvested from infected animals was significantly upregulated compared to that in pneumococci from glucose-containing medium. The SPD_0065 mutant strain was found to be attenuated in virulence in a manner specific to the host tissue.

Expression of four beta-galactosidases from Bifidobacterium bifidum NCIMB41171 and their contribution on the hydrolysis and synthesis of galactooligosaccharides

This paper deals with two aspects tightly related to the enzymatic characteristics and expression of four beta-galactosidases (BbgI, BbgII, BbgIII and BbgIV) from Bifidobacterium bifidum NCIMB41171. The growth patterns of this strain indicated a preference towards complex (i.e. lactose, galactooligosaccharides (GOSs)) rather than simple carbohydrates (i.e. glucose and galactose) and a collaborative action and synergistic relation of more than one beta-galactosidase isoenzyme for either lactose or GOS hydrolysis and subsequent assimilation. Native polyacrylamide gel electrophoresis analysis of protein extracts from cells growing on different carbohydrates (i.e. glucose, lactose or GOS) indicated that two lactose hydrolysing enzymes (BbgI and BbgIII) and one GOS hydrolysing enzyme (BbgII) were constitutively expressed, whereas a fourth lactose hydrolysing enzyme (BbgIV) was induced in the presence of lactose or different GOS fractions. Furthermore, the beta-galactosidase expression profiles of B. bifidum cells and the transgalactosylating properties of each individual isoenzyme, with lactose as substrate, clearly indicated that mainly three isoenzymes (BbgI, BbgIII and BbgIV) are implicated in GOS synthesis when whole B. bifidum cells are utilised. Two of the isoenzymes (BbgI and BbgIV) proved to have better transgalactosylating properties giving yields ranging from 42% to 47% whereas the rest (BbgI and BbgIII) showed lower yields (15% and 29%, respectively).