Santiago Ruiz-Moyano

Variation in consumption of human milk oligosaccharides by infant gut-associated strains of Bifidobacterium breve.

ABSTRACT Human milk contains a high concentration of complex oligosaccharides that influence the composition of the intestinal microbiota in breast-fed infants. Previous studies have indicated that select species such as Bifidobacterium longum subsp. infantis and Bifidobacterium bifidum can utilize human milk oligosaccharides (HMO) in vitro as the sole carbon source, while the relatively few B. longum subsp. longum and Bifidobacterium breve isolates tested appear less adapted to these substrates. Considering the high frequency at which B. breve is isolated from breast-fed infant feces, we postulated that some B. breve strains can more vigorously consume HMO and thus are enriched in the breast-fed infant gastrointestinal tract. To examine this, a number of B. breve isolates from breast-fed infant feces were characterized for the presence of different glycosyl hydrolases that participate in HMO utilization, as well as by their ability to grow on HMO or specific HMO species such as lacto-N-tetraose (LNT) and fucosyllactose. All B. breve strains showed high levels of growth on LNT and lacto-N-neotetraose (LNnT), and, in general, growth on total HMO was moderate for most of the strains, with several strain differences. Growth and consumption of fucosylated HMO were strain dependent, mostly in isolates possessing a glycosyl hydrolase family 29 α-fucosidase. Glycoprofiling of the spent supernatant after HMO fermentation by select strains revealed that all B. breve strains can utilize sialylated HMO to a certain extent, especially sialyl-lacto-N-tetraose. Interestingly, this specific oligosaccharide was depleted before neutral LNT by strain SC95. In aggregate, this work indicates that the HMO consumption phenotype in B. breve is variable; however, some strains display specific adaptations to these substrates, enabling more vigorous consumption of fucosylated and sialylated HMO. These results provide a rationale for the predominance of this species in breast-fed infant feces and contribute to a more accurate picture of the ecology of the developing infant intestinal microbiota.

Screening of lactic acid bacteria and bifidobacteria for potential probiotic use in Iberian dry fermented sausages

The purpose of this study was to select lactic acid bacteria and bifibobacteria strains as potential probiotic cultures during the processing of Iberian dry fermented sausages. A total of 1000 strains were isolated from Iberian dry fermented sausages (363), and human (337) and pig faeces (300) in different culture media. Around 30% of these strains, mainly isolated from Iberian dry fermented sausages in LAMVAB agar, were pre-selected for testing as potential probiotics by their ability to grow adequately at the pH values and NaCl concentrations of these meat products during the ripening process. Of the in vitro investigations used to predict the survival of a strain in conditions present in the gastro intestinal tract, exposure to pH 2.5 showed itself to be a highly discriminating factor with only 51 out of 312 pre-selected strains resisting adequately after 1.5h of exposure. All acid-resistant isolates identified as lactobacilli originated from human faeces (Lactobacillus casei and Lactobacillus fermentum) and pig faeces (Lactobacillus reuteri, Lactobacillus animalis, Lactobacillus murinus, and Lactobacillus vaginalis). Pediococcus acidilactici strains were isolated from Iberian dry fermented sausages and pig faeces, whereas the greatest number of Enterococcus strains were identified as Enterococcus faecium, with this species being isolated from Iberian dry fermented sausages, and human and pig faeces. Most of these strains are promising probiotic meat culture candidates suitable for Iberian dry fermented sausages.

Endo-β-N-acetylglucosaminidases from Infant Gut-associated Bifidobacteria Release Complex N-glycans from Human Milk Glycoproteins

Breastfeeding is one of the main factors guiding the composition of the infant gut microbiota in the first months of life. This process is shaped in part by the high amounts of human milk oligosaccharides that serve as a carbon source for saccharolytic bacteria such as Bifidobacterium species. Infant-borne bifidobacteria have developed various molecular strategies for utilizing these oligosaccharides as a carbon source. We hypothesized that these species also interact with N-glycans found in host glycoproteins that are structurally similar to free oligosaccharides in human milk. Endo-β-N-acetylglucosaminidases were identified in certain isolates of Bifidobacterium longum subsp. longum, B. longum subsp. infantis, and Bifidobacterium breve, and their presence correlated with the ability of these strains to deglycosylate glycoproteins. An endoglycosidase from B. infantis ATCC 15697, EndoBI-1, was active toward all major types of N-linked glycans found in glycosylated proteins. Its activity was not affected by core fucosylation or extensive fucosylation, antenna number, or sialylation, releasing several N-glycans from human lactoferrin and immunoglobulins A and G. Extensive N-deglycosylation of whole breast milk was also observed after coincubation with this enzyme. Mutation of the active site of EndoBI-1 did not abolish binding to N-glycosylated proteins, and this mutant specifically recognized Man3GlcNAc2(α1–6Fuc), the core structure of human N-glycans. EndoBI-1 is constitutively expressed in B. infantis, and incubation of the bacterium with human or bovine lactoferrin led to the induction of genes associated to import and consumption of human milk oligosaccharides, suggesting linked regulatory mechanisms among these glycans. This work reveals an unprecedented interaction of bifidobacteria with host N-glycans and describes a novel endoglycosidase with broad specificity on diverse N-glycan types, potentially a useful tool for glycoproteomics studies.

Application of Lactobacillus fermentum HL57 and Pediococcus acidilactici SP979 as potential probiotics in the manufacture of traditional Iberian dry-fermented sausages.

The purpose of this study was to investigate the potential of implanting the probiotics Lactobacillus fermentum HL57 and P. acidilactici SP979 during manufacture of Iberian dry-fermented sausages, and their effect on the sensory properties of these meat products. Microbial counts were studied in sausages inoculated with these strains and compared with a control batch. To detect the presence of probiotic strains at high counts (>7 log CFU/g) in the inoculated sausages, specific PCR and (RAPD)-PCR techniques were carried out. Changes due to probiotic inoculations on parameters and compounds related to fermentation, and nitrogen and lipid fractions were determined, and the impact on sensory quality evaluated by descriptive and hedonic tests. Iberian dry-fermented sausages inoculated with L. fermentum HL57 and P. acidilactici SP979 may be considered as functional products according to the counts of these strains found at the end of processing. However, inoculation with L. fermentum HL57 increased the amount of acetic acid and lipid degradation products such as malonaldehyde in Iberian dry-fermented sausages, resulting in a negative impact on relevant sensory parameters related to colour and taste. On the contrary, P. acidilactici SP979 did not notably modify the physicochemical parameters or the sensory quality of Iberian dry-fermented sausages when compared to the autochthonous microbial population present in the control batch.

Release and utilization of N-acetyl-d-glucosamine from human milk oligosaccharides by Bifidobacterium longum subsp. infantis

Human milk contains high amounts of complex oligosaccharides, which can be utilized especially by Bifidobacterium species in the infant gut as a carbon and energy source. N-acetyl-D-glucosamine is a building block of these oligosaccharides, and molecular details on the release and utilization of this monosaccharide are not fully understood. In this work we have studied some of the enzymatic properties of three N-acetyl-β-D-hexosaminidases encoded by the genome of the intestinal isolate Bifidobacterium longum subsp. infantis ATCC 15697 and the gene expression of the corresponding genes during bacterial growth on human milk oligosaccharides. These enzymes belong to the glycosyl hydrolase family 20, with several homologs in bifidobacteria. Their optimum pH was 5.0 and optimum temperature was 37 °C. The three enzymes were active on the GlcNAcβ1-3 linkage found in lacto-N-tetraose, the most abundant human milk oligosaccharide. Blon_0459 and Blon_0732, but not Blon_2355, cleaved branched GlcNAcβ1-6 linkages found in lacto-N-hexaose, another oligosaccharide abundant in breast milk. Bifidobacterium infantis N-acetyl-β-D-hexosaminidases were induced during early growth in vitro on human milk oligosaccharides, and also during growth on lacto-N-tetraose or lacto-N-neotetraose. The up-regulation of enzymes that convert this monosaccharide into UDP-N-acetylglucosamine by human milk oligosaccharides suggested that this activated sugar is used in peptidoglycan biosynthesis. These results emphasize the complexity of human milk oligosaccharide consumption by this infant intestinal isolate, and provide new clues into this process.

Rapid differentiation of lactic acid bacteria from autochthonous fermentation of Iberian dry-fermented sausages

The populations of lactic acid bacteria (LAB) in different types of Iberian dry-fermented sausages from central-west Spain were identified. A simple and rapid electrophoretic method of whole-cell protein profiles was evaluated, correlating it with 16S rRNA gene sequence analysis and biochemical identification by API 50 CHL. A total of 96 isolates were identified by SDS-PAGE showing stable profiles corresponding to 30-45 polypeptides in the range 95-8kDa that were clearly different for the different species and were grouped with those of the 9 reference strains used in this study. The SDS-PAGE method showed that the predominant species were Pediococcus acidilactici (48%) followed by Lactobacillus plantarum (23%) and Lactobacillus brevis (18%). The identifications obtained by this approach were confirmed by sequencing the V2-V3 region of the 16S rRNA gene and by a BLAST search of the GenBank database. However, biochemical identifications by API 50 CHL showed different errors at the genus and species level. In sum, the SDS-PAGE analysis showed itself to be a rapid and accurate differentiation method for the most commonly encountered LAB isolates in dry-fermented sausages.

Comparative transcriptomics reveals key differences in the response to milk oligosaccharides of infant gut-associated bifidobacteria.

Breast milk enhances the predominance of Bifidobacterium species in the infant gut, probably due to its large concentration of human milk oligosaccharides (HMO). Here we screened infant-gut isolates of Bifidobacterium longum subsp. infantis and Bifidobacterium bifidum using individual HMO, and compared the global transcriptomes of representative isolates on major HMO by RNA-seq. While B. infantis displayed homogeneous HMO-utilization patterns, B. bifidum were more diverse and some strains did not use fucosyllactose (FL) or sialyllactose (SL). Transcriptomes of B. bifidum SC555 and B. infantis ATCC 15697 showed that utilization of pooled HMO is similar to neutral HMO, while transcriptomes for growth on FL were more similar to lactose than HMO in B. bifidum. Genes linked to HMO-utilization were upregulated by neutral HMO and SL, but not by FL in both species. In contrast, FL induced the expression of alternative gene clusters in B. infantis. Results also suggest that B. bifidum SC555 does not utilize fucose or sialic acid from HMO. Surprisingly, expression of orthologous genes differed between both bifidobacteria even when grown on identical substrates. This study highlights two major strategies found in Bifidobacterium species to process HMO, and presents detailed information on the close relationship between HMO and infant-gut bifidobacteria.

Safety and functional aspects of pre-selected lactobacilli for probiotic use in Iberian dry-fermented sausages.

The purpose of this study was to investigate lactobacilli for potential probiotic use in Iberian dry-fermented sausages. A total of 18 strains, previously selected, isolated from different sources were evaluated according to safety and functional characteristics including biogenic amines and d-lactic acid production, antibiotic susceptibility, haemolysis, cell adhesion, and antimicrobial activity against food-borne pathogens. The strains Lactobacillus reuteri PL519, L. reuteri PL542, and Lactobacillus fermentum HL57 were able to establish their self on the intestinal epithelium, and an inhibition of such pathogenic bacteria as Listeria monocytogenesin vitro. These strains were also considered safe to be used with regard to their low aminogenic potential and d-lactic acid production, antibiotic resistance pattern and haemolytic activity. Thus, they were selected as a potential probiotic meat starter culture suitable for manufacture of dry-fermented Iberian sausages.

Safety and Functional Aspects of Preselected Enterococci for Probiotic Use in Iberian Dry-Fermented Sausages

The purpose of this study was to investigate enterococci for potential probiotic use in Iberian dry-fermented sausages. A total of 15 strains isolated from Iberian dry-fermented sausages, human feces, and pig feces were evaluated for their safety and functional characteristics including biogenic amine (BA) production, antibiotic susceptibility, hemolysis, virulence determinants, cell adhesion, and antimicrobial activity against foodborne pathogens. The strain Enterococcus faecium SE906 was able to establish itself on the intestinal epithelium, inhibiting such pathogenic bacteria as Listeria monocytogenes in vitro. This strain was also considered safe to be used for its low aminogenic potential, and its antibiotic resistance pattern and virulence determinants, being identified as a potential probiotic meat starter culture suitable for manufacture of dry-fermented Iberian sausages.

A novel gene cluster allows preferential utilization of fucosylated milk oligosaccharides in Bifidobacterium longum subsp. longum SC596

The infant intestinal microbiota is often colonized by two subspecies of Bifidobacterium longum: subsp. infantis (B. infantis) and subsp. longum (B. longum). Competitive growth of B. infantis in the neonate intestine has been linked to the utilization of human milk oligosaccharides (HMO). However, little is known how B. longum consumes HMO. In this study, infant-borne B. longum strains exhibited varying HMO growth phenotypes. While all strains efficiently utilized lacto-N-tetraose, certain strains additionally metabolized fucosylated HMO. B. longum SC596 grew vigorously on HMO, and glycoprofiling revealed a preference for consumption of fucosylated HMO. Transcriptomes of SC596 during early-stage growth on HMO were more similar to growth on fucosyllactose, transiting later to a pattern similar to growth on neutral HMO. B. longum SC596 contains a novel gene cluster devoted to the utilization of fucosylated HMO, including genes for import of fucosylated molecules, fucose metabolism and two α-fucosidases. This cluster showed a modular induction during early growth on HMO and fucosyllactose. This work clarifies the genomic and physiological variation of infant-borne B. longum to HMO consumption, which resembles B. infantis. The capability to preferentially consume fucosylated HMO suggests a competitive advantage for these unique B. longum strains in the breast-fed infant gut.