Starch and starch hydrolysates are favorable carbon sources for bifidobacteria in the human gut

Unveiling metabolic pathways of selected plant-derived glycans by Bifidobacterium pseudocatenulatum

Bifidobacteria are commonly encountered members of the human gut microbiota that possess the enzymatic machinery necessary for the metabolism of certain plant-derived, complex carbohydrates. In the current study we describe differential growth profiles elicited by a panel of 21 newly isolated Bifidobacterium pseudocatenulatum strains on various plant-derived glycans. Using a combination of gene-trait matching and comparative genome analysis, we identified two distinct xylanases responsible for the degradation of xylan. Furthermore, three distinct extracellular α-amylases were shown to be involved in starch degradation by certain strains of B. pseudocatenulatum. Biochemical characterization showed that all three α-amylases can cleave the related substrates amylose, amylopectin, maltodextrin, glycogen and starch. The genes encoding these enzymes are variably found in the species B. pseudocatenulatum, therefore constituting a strain-specific adaptation to the gut environment as these glycans constitute common plant-derived carbohydrates present in the human diet. Overall, our study provides insights into the metabolism of these common dietary carbohydrates by a human-derived bifidobacterial species.

Resistant starch utilization by Bifidobacterium, the beneficial human gut bacteria

Resistant starch (RS) reaches the large intestine largely intact, where it is fermented by the gut microbiota, resulting in the production of short-chain fatty acids (SCFAs) that have beneficial effects on the human body. Bifidobacteria are a major species widely used in the probiotic field, and are increased in the gut by RS, indicating their importance in RS metabolism in the intestine. Bifidobacteria have a genetic advantage in starch metabolism as they possess a significant number of starch-degrading enzymes and extraordinary three RS-degrading enzymes, allowing them to utilize RS. However, to date, only three species of RS-degrading bifidobacteria have been reported as single isolates B. adolescentis, B. choerinum, and B. pseudolongum. In this review, we describe recent studies on RS utilization by Bifidobacterium, based on their biochemical characteristics and genetic findings. This review provides a crucial understanding of how bifidobacteria survive in specific niches with abundant RS such as the human gut.

Effects of Bifidobacteria Fermentation on Physico-Chemical, Thermal and Structural Properties of Wheat Starch

Lactic acid bacteria have been considered to be a very important species during sourdough fermentation. In order to explore the effects of bifidobacteria fermentation on thermal, physico-chemical and structural properties of wheat starch during dough fermentation, starch granules were separated from the fermented dough at different fermentation times, including 0 h, 2 h, 6 h, 9 h and 12 h. The results showed that the morphology of starch granules was destroyed gradually as the fermentation time increased, which appeared as erosion and rupture. With the increase in fermentation time, the solubility showed a significant increase, which changed from 8.51% (0 h) to 9.80% (12 h), and the swelling power was also increased from 9.31% (0 h) to 10.54% (12 h). As for the gelatinization property, the enthalpy was increased from 6.77 J/g (0 h) to 7.56 J/g (12 h), indicating a more stable thermal property of fermented starch, especially for the longer fermentation. The setback value was decreased with short fermentation time, indicating that the starch with a longer fermentation time was difficult to retrograde. The hardness of the gel texture was decreased significantly from 50.11 g to 38.66 g after fermentation for 12 h. The results show that bifidobacteria fermentation is an effective biological modification method of wheat starch for further applications.

A cross-sectional analysis from the Mykinso Cohort Study: establishing reference ranges for Japanese gut microbial indices

The purpose of this study was to establish reference ranges for gut microbial indices by collecting real-world Japanese microbiome data from a Mykinso cohort. Although several large cohort studies have focused on the human gut microbiome, large cohort studies of the gut microbiome from Japanese populations are scarce, especially from healthy or non-diseased individuals. We collected stool samples and original survey lifestyle information from 5,843 Japanese individuals through the Mykinso gut microbiome testing service. From the obtained 16S rRNA sequence data derived from stool samples, the ratio and distribution of each taxon were analyzed. The relationship between different epidemiological attributes and gut microbial indicators were statistically analyzed. The qualitative and quantitative indicators of these common gut microbiota were confirmed to be strongly correlated with age, sex, constipation/diarrhea, and history of lifestyle-related diseases. Therefore, we set up a healthy sub-cohort that controlled for these attribute factors and defined reference ranges from the distribution of gut microbial index in that population. Taken together, these results show that the gut microbiota of Japanese people had high beta-diversity, with no single "typical" gut microbiota type. We believe that the reference ranges for the gut microbial indices obtained in this study can be new reference values for determining the balance and health of the gut microbiota of an individual. In the future, it is necessary to clarify the clinical validity of these reference values by comparing them with a clinical disease cohort.

Understanding the host-microbe interactions using metabolic modeling

The human gut harbors an enormous number of symbiotic microbes, which is vital for human health. However, interactions within the complex microbiota community and between the microbiota and its host are challenging to elucidate, limiting development in the treatment for a variety of diseases associated with microbiota dysbiosis. Using in silico simulation methods based on flux balance analysis, those interactions can be better investigated. Flux balance analysis uses an annotated genome-scale reconstruction of a metabolic network to determine the distribution of metabolic fluxes that represent the complete metabolism of a bacterium in a certain metabolic environment such as the gut. Simulation of a set of bacterial species in a shared metabolic environment can enable the study of the effect of numerous perturbations, such as dietary changes or addition of a probiotic species in a personalized manner. This review aims to introduce to experimental biologists the possible applications of flux balance analysis in the host-microbiota interaction field and discusses its potential use to improve human health. Video abstract.

Gut Biofactory-Neurocompetent Metabolites within the Gastrointestinal Tract. A Scoping Review

The gut microbiota have gained much scientific attention recently. Apart from unravelling the taxonomic data, we should understand how the altered microbiota structure corresponds to functions of this complex ecosystem. The metabolites of intestinal microorganisms, especially bacteria, exert pleiotropic effects on the human organism and contribute to the host systemic balance. These molecules play key roles in regulating immune and metabolic processes. A subset of them affect the gut brain axis signaling and balance the mental wellbeing. Neurotransmitters, short chain fatty acids, tryptophan catabolites, bile acids and phosphatidylcholine, choline, serotonin, and L-carnitine metabolites possess high neuroactive potential. A scoping literature search in PubMed/Embase was conducted up until 20 June 2020, using three major search terms "microbiota metabolites" AND "gut brain axis" AND "mental health". This review aimed to enhance our knowledge regarding the gut microbiota functional capacity, and support current and future attempts to create new compounds for future clinical interventions.

Mouse Abdominal Fat Depots Reduced by Butyric Acid-Producing Leuconostoc mesenteroides

The activation of peroxisome proliferator-activated rece ptor gamma (PPAR-γ) is known to induce the differentiation of adipocytes. This study aimed to investigate the probiotic effect of Leuconostoc mesenteroides (L. mesenteroides) on high-fat diet (HFD)-induced PPAR-γ activation and abdominal fat depots. Incubation of differentiated 3T3-L1 adipocytes with media of L. mesenteroides EH-1, a butyric acid-producing strain, significantly reduced the amounts of lipid droplets. The oral administration of L. mesenteroides EH-1 produced large amounts (>1 mM) of butyric acid in cecum and attenuated the HFD-induced upregulation of PPAR-γ and accumulation of abdominal fats in mice. The combination of 2% glucose with L. mesenteroides EH-1 increased the production of butyric acid and potentiated the probiotic activity of L. mesenteroides EH-1 against the formation of lipid droplets in 3T3-L1 adipocytes as well as abdominal fats in HFD-fed mice. The inhibition of free fatty acid receptor 2 (Ffar2) by its antagonist, GLPG-0974, markedly diminished the probiotic effects of L. mesenteroides EH-1 plus glucose on the suppression of HFD-induced PPAR-γ and abdominal fats. Besides demonstrating the probiotic value of L. mesenteroides EH-1, our results highlight the possible therapy targeting the butyric acid-activated Ffar2 pathway to reduce abdominal fats.

Bifidobacterium tibiigranuli sp. nov. isolated from homemade water kefir

Two Bifidobacterium strains, TMW 2.2057^T and TMW 2.1764 were isolated from two different homemade water kefirs from Germany. Both strains were oxidase- and catalase-negative and Gram-staining-positive. Cells were non-motile, irregular rods that were aerotolerant anaerobes. On basis of fructose 6-phosphate phosphoketolase activity, they were assigned to the family Bifidobacteriaceae. Comparative analysis of 16S rRNA and concatenated housekeeping genes (clpC, dnaB, dnaG, dnaJ, hsp60 and rpoB) demonstrated that both strains represented a member of the genus Bifidobacterium, with Bifidobacterium subtile DSM 20096^T as the closest phylogenetic relative (98.35 % identity). Both strains can be distinguished using randomly amplified polymorphic DNA fingerprinting. Analysis of concatenated marker gene sequences as well as average nucleotide identity by blast (ANIb) and in silico DNA-DNA hybridization (isDDH) calculations of their genome sequences confirmed Bifidobacterium subtile DSM 20096^T as the closest relative (87.91 and 35.80 % respectively). All phylogenetic analyses allow differentiation of strains TMW 2.2057^T and TMW 2.1764 from all hitherto described species of the genus Bifidobacterium with validly published names. We therefore propose a novel species with the name Bifidobacterium tibiigranuli, for which TMW 2.2057^T (=DSM 108414^T=LMG 31086^T) is the type strain.

Complete genome sequence of Bifidobacterium adolescentis P2P3, a human gut bacterium possessing strong resistant starch-degrading activity

Resistant starch (RS) is an important food source from which gut bacteria produce short chain fatty acids, which have beneficial effects for human health. The Bifidobacterium adolescentis P2P3, a human gut bacterium possessing a strong RS-degrading activity, was isolated from a healthy Korean adult male. In vitro experiments showed that this bacterium could utilize approximately 63% of high amylose corn starch after forming RS granule clusters. Here we provide the first complete set of genomic information on RS-degrading B. adolescentis P2P3. The genome of B. adolescentis P2P3 consists of one chromosome (2,202,982 bp) with high GC content (59.4%). Analysis of the protein-coding genes revealed that at least nineteen of the starch degradation-related enzymes were present in the genome. Among those, five genes evidently possess carbohydrate-binding domains, which are presumed to be involved in efficient RS decomposition. The complete set of genomic information on B. adolescentis P2P3 could provide an understanding of the role of RS-degrading gut bacteria and its RS degradation mechanism.

Evolutionary relationships among bifidobacteria and their hosts and environments

BACKGROUND

The assembly of animal microbiomes is influenced by multiple environmental factors and host genetics, although the relative importance of these factors remains unclear. Bifidobacteria (genus Bifidobacterium, phylum Actinobacteria) are common first colonizers of gut microbiomes in humans and inhabit other mammals, social insects, food, and sewages. In humans, the presence of bifidobacteria in the gut has been correlated with health-promoting benefits. Here, we compared the genome sequences of a subset of the over 400 Bifidobacterium strains publicly available to investigate the adaptation of bifidobacteria diversity. We tested 1) whether bifidobacteria show a phylogenetic signal with their isolation sources (hosts and environments) and 2) whether key traits encoded by the bifidobacteria genomes depend on the host or environment from which they were isolated. We analyzed Bifidobacterium genomes available in the PATRIC and NCBI repositories and identified the hosts and/or environment from which they were isolated. A multilocus phylogenetic analysis was conducted to compare the genetic relatedness the strains harbored by different hosts and environments. Furthermore, we examined differences in genomic traits and genes related to amino acid biosynthesis and degradation of carbohydrates.

RESULTS

We found that bifidobacteria diversity appears to have evolved with their hosts as strains isolated from the same host were non-randomly associated with their phylogenetic relatedness. Moreover, bifidobacteria isolated from different sources displayed differences in genomic traits such as genome size and accessory gene composition and on particular traits related to amino acid production and degradation of carbohydrates. In contrast, when analyzing diversity within human-derived bifidobacteria, we observed no phylogenetic signal or differences on specific traits (amino acid biosynthesis genes and CAZymes).

CONCLUSIONS

Overall, our study shows that bifidobacteria diversity is strongly adapted to specific hosts and environments and that several genomic traits were associated with their isolation sources. However, this signal is not observed in human-derived strains alone. Looking into the genomic signatures of bifidobacteria strains in different environments can give insights into how this bacterial group adapts to their environment and what types of traits are important for these adaptations.

What Is the Impact of Diet on Nutritional Diarrhea Associated with Gut Microbiota in Weaning Piglets: A System Review

Piglets experience severe growth challenges and diarrhea after weaning due to nutritional, social, psychological, environmental, and physiological changes. Among these changes, the nutritional factor plays a key role in postweaning health. Dietary protein, fibre, starch, and electrolyte levels are highly associated with postweaning nutrition diarrhea (PWND). In this review, we mainly discuss the high protein, fibre, resistant starch, and electrolyte imbalance in diets that induce PWND, with a focus on potential mechanisms in weaned piglets.

Deciphering the metabolic capabilities of Bifidobacteria using genome-scale metabolic models

Bifidobacteria, the initial colonisers of breastfed infant guts, are considered as the key commensals that promote a healthy gastrointestinal tract. However, little is known about the key metabolic differences between different strains of these bifidobacteria, and consequently, their suitability for their varied commercial applications. In this context, the present study applies a constraint-based modelling approach to differentiate between 36 important bifidobacterial strains, enhancing their genome-scale metabolic models obtained from the AGORA (Assembly of Gut Organisms through Reconstruction and Analysis) resource. By studying various growth and metabolic capabilities in these enhanced genome-scale models across 30 different nutrient environments, we classified the bifidobacteria into three specific groups. We also studied the ability of the different strains to produce short-chain fatty acids, finding that acetate production is niche- and strain-specific, unlike lactate. Further, we captured the role of critical enzymes from the bifid shunt pathway, which was found to be essential for a subset of bifidobacterial strains. Our findings underline the significance of analysing metabolic capabilities as a powerful approach to explore distinct properties of the gut microbiome. Overall, our study presents several insights into the nutritional lifestyles of bifidobacteria and could potentially be leveraged to design species/strain-specific probiotics or prebiotics.

Probiotic Properties of Lactobacillus paracasei subsp. paracasei L1 and Its Growth Performance-Promotion in Chicken by Improving the Intestinal Microflora

Lactobacillus paracasei subsp. paracasei L1 was previously isolated from sweet potato sour liquid. This bacterial species specifically binds onto starch granular surfaces, triggering the enzymatic hydrolysis of raw starch. We investigated the functional and safety properties of strain L1 in vitro to establish its probiotic potential, and analyzed its effect on growth performance and intestinal microflora of chicken in feeding experiments. The optimal growth conditions of strain L1 included low pH and high concentrations of bile salts and NaCl. Its 1-, 2-, and 24-h autoaggregation values were 15.8 ± 1.2%, 20.4 ± 2.3%, and 47.2 ± 0.8%, respectively, with the surface hydrophobicity value at 560 nm of 38.1 ± 2.7%. Further, its adhesion rate to Caco-2 cells was 22.37 ± 1.44%. Strain L1 was resistant to erythromycin and azithromycin, but sensitive to other antibiotics tested. For the feeding experiments, 240 chickens with similar weights were randomly divided into a control (C) group and strain L1 (L) group and fed for 8 weeks. Strain L1 promoted the weight gain of chickens in L group. A significant increase in the population size of the two phyla and 23 genera in the small intestine was observed in the presence of strain L1 (P < 0.05), with 0 phyla and 4 genera showing significant increase in the cecum (P < 0.05). In the small intestine, the abundance of six functional genes at Kyoto Encyclopedia of Genes and Genomes (KEGG) level 2 and 49 genes at KEGG level 3 was significantly increased in group L (P < 0.05), with lesser changes noted in the cecum. An increase in the metabolic pathway functions, including enzyme families and the digestive system, was observed in the intestinal microbiota in the L group compared to the C group. However, the other metabolic pathway functions, including metabolism of fatty acid biosynthesis, as well as metabolism of glycerolipids and propanoate, increased in the cecal microbiota of the L group relative to the C group. These changes are most likely related to the changes in the gut microbiota composition. Collectively, strain L1 supplementation may promote growth performance and improve the intestinal microflora in chicken although further studies are needed to confirm this.

The Capacity of the Fecal Microbiota From Malawian Infants to Ferment Resistant Starch

In Low and Middle-Income Countries (LMIC), weaning is associated with environmentally acquired and inflammation-associated enteric disorders. Dietary intake of high amylose maize starch (HAMS) can promote commensal fermentative bacteria and drive the production of short chain fatty acids (SCFAs). By stabilizing commensal gut microbiology, and stimulating the production of anti-inflammatory metabolites, HAMS supplementation might therefore influence enteric health. However, the extent to which the gut microbiota of LMIC infants are capable of fermenting HAMS is unclear. We assessed the capacity of the fecal microbiota from pre-weaning and weaning Malawian infants to ferment HAMS and produce SCFAs using an in vitro fermentation model. Fecal microbiota from both pre-weaning and weaning infants were able to ferment HAMS, as indicated by an increase in bacterial load and total SCFA concentration, and a reduction in pH. All of these changes were more substantial in the weaning group. Acetate production was observed with both pre-weaning and weaning groups, while propionate production was only observed in the weaning group. HAMS fermentation resulted in significant alterations to the fecal microbial community in the weaning group, with significant increases in levels of Prevotella, Veillonella, and Collinsella associated with propionate production. In conclusion, fecal microbiota from Malawian infants before and during weaning has the capacity to produce acetate through HAMS fermentation, with propionate biosynthetic capability appearing only at weaning. Our results suggest that HAMS supplementation might provide benefit to infants during weaning.

Systematic Review of Gut Microbiota and Major Depression

Background: Recently discovered relationships between the gastrointestinal microbiome and the brain have implications for psychiatric disorders, including major depressive disorder (MDD). Bacterial transplantation from MDD patients to rodents produces depression-like behaviors. In humans, case-control studies have examined the gut microbiome in healthy and affected individuals. We systematically reviewed existing studies comparing gut microbial composition in MDD and healthy volunteers. Methods: A PubMed literature search combined the terms "depression," "depressive disorder," "stool," "fecal," "gut," and "microbiome" to identify human case-control studies that investigated relationships between MDD and microbiota quantified from stool. We evaluated the resulting studies, focusing on bacterial taxa that were different between MDD and healthy controls. Results: Six eligible studies were found in which 50 taxa exhibited differences (p < 0.05) between patients with MDD and controls. Patient characteristics and methodologies varied widely between studies. Five phyla-Bacteroidetes, Firmicutes, Actinobacteria, Fusobacteria, and Protobacteria-were represented; however, divergent results occurred across studies for all phyla. The largest number of differentiating taxa were within phylum Firmicutes, in which nine families and 12 genera differentiated the diagnostic groups. The majority of these families and genera were found to be statistically different between the two groups in two identified studies. Family Lachnospiraceae differentiated the diagnostic groups in four studies (with an even split in directionality). Across all five phyla, nine genera were higher in MDD (Anaerostipes, Blautia, Clostridium, Klebsiella, Lachnospiraceae incertae sedis, Parabacteroides, Parasutterella, Phascolarctobacterium, and Streptococcus), six were lower (Bifidobacterium, Dialister, Escherichia/Shigella, Faecalibacterium, and Ruminococcus), and six were divergent (Alistipes, Bacteroides, Megamonas, Oscillibacter, Prevotella, and Roseburia). We highlight mechanisms and products of bacterial metabolism as they may relate to the etiology of depression. Conclusions: No consensus has emerged from existing human studies of depression and gut microbiome concerning which bacterial taxa are most relevant to depression. This may in part be due to differences in study design. Given that bacterial functions are conserved across taxonomic groups, we propose that studying microbial functioning may be more productive than a purely taxonomic approach to understanding the gut microbiome in depression.

Starch Malabsorption in Infants

Based on the developmental physiology of pancreatic amylase production, starch digestion in young infants was anticipated to be compromised whenever compared with that in older infants and toddlers. This appears to be the case, but with great variability among infants to digest starch. Evidence points to the importance of maltase-glucoamylase in young infants and its effect on starch digestion. These observations have critical importance for recommendations regarding the feeding of starch-containing foods to young infants.

The effect of resistant starch (RS) on the bovine rumen microflora and isolation of RS-degrading bacteria

Resistant starch (RS) in the diet reaches the large intestine without degradation, where it is decomposed by the commensal microbiota. The fermentation of RS produces secondary metabolites including short-chain fatty acids (SCFAs), which have been linked to a variety of physiological and health effects. Therefore, the availability of RS as a prebiotic is a current issue. The objectives of this study were (1) to use metagenomics to observe microbial flora changes in Bos taurus coreanae rumen fluid in the presence of RS and (2) to isolate RS-degrading microorganisms. The major microbial genus in a general rumen fluid was Succiniclasticum sp., whereas Streptococcus sp. immediately predominated after the addition of RS into the culture medium and was then drastically replaced by Lactobacillus sp. The presence of Bifidobacterium sp. was also observed continuously. Several microorganisms with high RS granule-degrading activity were identified and isolated, including B. choerinum FMB-1 and B. pseudolongum FMB-2. B. choerinum FMB-1 showed the highest RS-hydrolyzing activity and degraded almost 60% of all substrates tested. Coculture experiments demonstrated that Lactobacillus brevis ATCC 14869, which was isolated from human feces, could grow using reducing sugars generated from RS by B. choerinum FMB-1. These results suggest that Bifidobacterium spp., especially B. choerinum FMB-1, are the putative primary degrader of RS in rumen microbial flora and could be further studied as probiotic candidates.

Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains

Background

Bifidobacterium longum is a common member of the human gut microbiota and is frequently present at high numbers in the gut microbiota of humans throughout life, thus indicative of a close symbiotic host-microbe relationship. Different mechanisms may be responsible for the high competitiveness of this taxon in its human host to allow stable establishment in the complex and dynamic intestinal microbiota environment. The objective of this study was to assess the genetic and metabolic diversity in a set of 20 B. longum strains, most of which had previously been isolated from infants, by performing whole genome sequencing and comparative analysis, and to analyse their carbohydrate utilization abilities using a gene-trait matching approach.

Results

We analysed their pan-genome and their phylogenetic relatedness. All strains clustered in the B. longum ssp. longum phylogenetic subgroup, except for one individual strain which was found to cluster in the B. longum ssp. suis phylogenetic group. The examined strains exhibit genomic diversity, while they also varied in their sugar utilization profiles. This allowed us to perform a gene-trait matching exercise enabling the identification of five gene clusters involved in the utilization of xylo-oligosaccharides, arabinan, arabinoxylan, galactan and fucosyllactose, the latter of which is an abundant human milk oligosaccharide (HMO).

Conclusions

The results showed high diversity in terms of genes and predicted glycosyl-hydrolases, as well as the ability to metabolize a large range of sugars. Moreover, we corroborate the capability of B. longum ssp. longum to metabolise HMOs. Ultimately, their intraspecific genomic diversity and the ability to consume a wide assortment of carbohydrates, ranging from plant-derived carbohydrates to HMOs, may provide an explanation for the competitive advantage and persistence of B. longum in the human gut microbiome.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4388-9) contains supplementary material, which is available to authorized users.

Mucin Cross-Feeding of Infant Bifidobacteria and Eubacterium hallii

Mucus production is initiated before birth and provides mucin glycans to the infant gut microbiota. Bifidobacteria are the major bacterial group in the feces of vaginally delivered and breast milk-fed infants. Among the bifidobacteria, only Bifidobacterium bifidum is able to degrade mucin and to release monosaccharides which can be used by other gut microbes colonizing the infant gut. Eubacterium hallii is an early occurring commensal that produces butyrate and propionate from fermentation metabolites but that cannot degrade complex oligo- and polysaccharides. We aimed to demonstrate that mucin cross-feeding initiated by B. bifidum enables growth and metabolite formation of E. hallii leading to short-chain fatty acid (SCFA) formation. Growth and metabolite formation of co-cultures of B. bifidum, of Bifidobacterium breve or Bifidobacterium infantis, which use mucin-derived hexoses and fucose, and of E. hallii were determined. Growth of E. hallii in the presence of lactose and mucin monosaccharides was tested. In co-culture fermentations, the presence of B. bifidum enabled growth of the other strains. B. bifidum/B. infantis co-cultures yielded acetate, formate, and lactate while co-cultures of B. bifidum and E. hallii formed acetate, formate, and butyrate. In three-strain co-cultures, B. bifidum, E. hallii, and B. breve or B. infantis produced up to 16 mM acetate, 5 mM formate, and 4 mM butyrate. The formation of propionate (approximately 1 mM) indicated cross-feeding on fucose. Lactose, galactose, and GlcNAc were identified as substrates of E. hallii. This study shows that trophic interactions of bifidobacteria and E. hallii lead to the formation of acetate, butyrate, propionate, and formate, potentially contributing to intestinal SCFA formation with potential benefits for the host and for microbial colonization of the infant gut. The ratios of SCFA formed differed depending on the microbial species involved in mucin cross-feeding.

Development of a Synbiotic Beverage Enriched with Bifidobacteria Strains and Fortified with Whey Proteins

The objective of this study was to develop a new synbiotic beverage evaluating the ability of some bifidobacteria strains to grow in this beverage which was fortified with whey proteins up to 20 g L^-1, and enriched with 10 g L^-1 of prebiotic inulin or resistant starch. The ability of Bifidobacterium strains to survive for 30 days at 4°C was evaluated in two synbiotic whey protein fortified beverages formulated with 2% of whey proteins and 1% of inulin or resistant starch. Microbial growth was significantly affected by the whey protein amount as well as by the kind of prebiotic fiber. Resistant starch promoted the growth of the Bifidobacterium pseudocatenulatum strain and its viability under cold storage, also conferring higher sensory scores. The development of this new functional beverage will allow to carry out in vivo trials in order to validate its pre- and probiotic effects.

Microscale spatial analysis provides evidence for adhesive monopolization of dietary nutrients by specific intestinal bacteria

Each species of intestinal bacteria requires a nutritional source to maintain its population in the intestine. Dietary factors are considered to be major nutrients; however, evidence directly explaining the in situ utilization of dietary factors is limited. Microscale bacterial distribution would provide clues to understand bacterial lifestyle and nutrient utilization. However, the detailed bacterial localization around dietary factors in the intestine remains uninvestigated. Therefore, we explored microscale habitats in the murine intestine by using histology and fluorescent in situ hybridization, focusing on dietary factors. This approach successfully revealed several types of bacterial colonization. In particular, bifidobacterial colonization and adhesion on granular starch was frequently and commonly observed in the jejunum and distal colon. To identify the bacterial composition of areas around starch granules and areas without starch, laser microdissection and next-generation sequencing-based 16S rRNA microbial profiling was performed. It was found that Bifidobacteriaceae were significantly enriched by 4.7 fold in peri-starch areas compared to ex-starch areas. This family solely consisted of Bifidobacterium pseudolongum. In contrast, there was no significant enrichment among the other major families. This murine intestinal B. pseudolongum had starch-degrading activity, confirmed by isolation from the mouse feces and in vitro analysis. Collectively, our results demonstrate the significance of starch granules as a major habitat and potential nutritional niche for murine intestinal B. pseudolongum. Moreover, our results suggest that colonizing bifidobacteria effectively utilize starch from the closest location and maintain the location. This may be a bacterial strategy to monopolize solid dietary nutrients. We believe that our analytical approach could possibly be applied to other nutritional factors, and can be a powerful tool to investigate in vivo relationships between bacteria and environmental factors in the intestine.

Fucosyllactose and L-fucose utilization of infant Bifidobacterium longum and Bifidobacterium kashiwanohense

Background

Human milk oligosaccharides (HMOs) are one of the major glycan source of the infant gut microbiota. The two species that predominate the infant bifidobacteria community, Bifidobacterium longum subsp. infantis and Bifidobacterium bifidum, possess an arsenal of enzymes including α-fucosidases, sialidases, and β-galactosidases to metabolise HMOs. Recently bifidobacteria were obtained from the stool of six month old Kenyan infants including species such as Bifidobacterium kashiwanohense, and Bifidobacterium pseudolongum that are not frequently isolated from infant stool.

The aim of this study was to characterize HMOs utilization by these isolates. Strains were grown in presence of 2′-fucosyllactose (2′-FL), 3′-fucosyllactose (3′-FL), 3′-sialyl-lactose (3′-SL), 6′-sialyl-lactose (6′-SL), and Lacto-N-neotetraose (LNnT). We further investigated metabolites formed during L-fucose and fucosyllactose utilization, and aimed to identify genes and pathways involved through genome comparison.

Results

Bifidobacterium longum subsp. infantis isolates, Bifidobacterium longum subsp. suis BSM11-5 and B. kashiwanohense strains grew in the presence of 2′-FL and 3′- FL. All B. longum isolates utilized the L-fucose moiety, while B. kashiwanohense accumulated L-fucose in the supernatant. 1,2-propanediol (1,2-PD) was the major metabolite from L-fucose fermentation, and was formed in equimolar amounts by B. longum isolates.

Alpha-fucosidases were detected in all strains that degraded fucosyllactose. B. longum subsp. infantis TPY11-2 harboured four α-fucosidases with 95–99 % similarity to the type strain. B. kashiwanohense DSM 21854 and PV20-2 possessed three and one α-fucosidase, respectively. The two α-fucosidases of B. longum subsp. suis were 78–80 % similar to B. longum subsp. infantis and were highly similar to B. kashiwanohense α-fucosidases (95–99 %). The genomes of B. longum strains that were capable of utilizing L-fucose harboured two gene regions that encoded enzymes predicted to metabolize L-fucose to L-lactaldehyde, the precursor of 1,2-PD, via non-phosphorylated intermediates.

Conclusion

Here we observed that the ability to utilize fucosyllactose is a trait of various bifidobacteria species. For the first time, strains of B. longum subsp. infantis and an isolate of B. longum subsp. suis were shown to use L-fucose to form 1,2-PD. As 1,2-PD is a precursor for intestinal propionate formation, bifidobacterial L-fucose utilization may impact intestinal short chain fatty acid balance. A L-fucose utilization pathway for bifidobacteria is suggested.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0867-4) contains supplementary material, which is available to authorized users.

Mothers Secretor Status Affects Development of Childrens Microbiota Composition and Function: A Pilot Study

Background

One mechanism by which early life environment may influence long term health is through modulation of the gut microbiota. It is widely accepted that the optimal source of nutrition in early life is breast milk, with Human Milk Oligosaccharides (HMOs) thought to play an important role in nourishing the developing microbiota. However, mothers with inactive secretor genes have altered HMO composition and quantities in their breast milk. In this pilot study we examine the influence of secretor status and breast-feeding on microbiota composition at 2 to 3 years of age.

Methods

37 children and 17 eligible mothers were recruited. Secretor status was determined from blood and saliva samples using hemagglutination inhibition technique and faecal microbiota composition was examined by 16S rRNA gene sequencing.

Results

Secretor status was determined for 28 eligible children with 20 being secretors (S, 71.4%). Eleven of the 17 mothers were secretors (S, 64.7%). Unweighted UniFrac distances were significantly associated with child secretor status (R² = 0.069, p = 0.030) and with mother secretor status in children exclusively breastfed for at least 4 months (R² = 0.167, p = 0.028), suggesting an influence on the presence/absence of microbes, with Prevotella not detected in samples from secretor children and children of secretor mothers. In children who were exclusively breast-fed for at least 4 months of life the abundance of the known HMO consumers Bifidobacterium were increased in the children of secretor mothers compared to non-secretor mothers. The relative abundance of an OTU related to Bacteroides plebeius, a bacterium noted for its capacity to utilise sulphated polysaccharides for growth, was decreased in these children.

Conclusions

Child and mothers’ secretor status have an impact on childrens’ microbiota composition at 2 to 3 years of age.

Proteinaceous Molecules Mediating Bifidobacterium-Host Interactions

Bifidobacteria are commensal microoganisms found in the gastrointestinal tract. Several strains have been attributed beneficial traits at local and systemic levels, through pathogen exclusion or immune modulation, among other benefits. This has promoted a growing industrial and scientific interest in bifidobacteria as probiotic supplements. However, the molecular mechanisms mediating this cross-talk with the human host remain unknown. High-throughput technologies, from functional genomics to transcriptomics, proteomics, and interactomics coupled to the development of both in vitro and in vivo models to study the dynamics of the intestinal microbiota and their effects on host cells, have eased the identification of key molecules in these interactions. Numerous secreted or surface-associated proteins or peptides have been identified as potential mediators of bifidobacteria-host interactions and molecular cross-talk, directly participating in sensing environmental factors, promoting intestinal colonization, or mediating a dialogue with mucosa-associated immune cells. On the other hand, bifidobacteria induce the production of proteins in the intestine, by epithelial or immune cells, and other gut bacteria, which are key elements in orchestrating interactions among bifidobacteria, gut microbiota, and host cells. This review aims to give a comprehensive overview on proteinaceous molecules described and characterized to date, as mediators of the dynamic interplay between bifidobacteria and the human host, providing a framework to identify knowledge gaps and future research needs.

The gut microbiome of healthy Japanese and its microbial and functional uniqueness

The human gut microbiome has profound influences on the host's health largely through its interference with various intestinal functions. As recent studies have suggested diversity in the human gut microbiome among human populations, it will be interesting to analyse how gut microbiome is correlated with geographical, cultural, and traditional differences. The Japanese people are known to have several characteristic features such as eating a variety of traditional foods and exhibiting a low BMI and long life span. In this study, we analysed gut microbiomes of the Japanese by comparing the metagenomic data obtained from 106 Japanese individuals with those from 11 other nations. We found that the composition of the Japanese gut microbiome showed more abundant in the phylum Actinobacteria, in particular in the genus Bifidobacterium, than other nations. Regarding the microbial functions, those of carbohydrate metabolism were overrepresented with a concurrent decrease in those for replication and repair, and cell motility. The remarkable low prevalence of genes for methanogenesis with a significant depletion of the archaeon Methanobrevibacter smithii and enrichment of acetogenesis genes in the Japanese gut microbiome compared with others suggested a difference in the hydrogen metabolism pathway in the gut between them. It thus seems that the gut microbiome of the Japanese is considerably different from those of other populations, which cannot be simply explained by diet alone. We postulate possible existence of hitherto unknown factors contributing to the population-level diversity in human gut microbiomes.

Proteomic Profiling of Bifidobacterium bifidum S17 Cultivated Under In Vitro Conditions

Bifidobacteria are frequently used in probiotic food and dairy products. Bifidobacterium bifidum S17 is a promising probiotic candidate strain that displays strong adhesion to intestinal epithelial cells and elicits potent anti-inflammatory capacity both in vitro and in murine models of colitis. The recently sequenced genome of B. bifidum S17 has a size of about 2.2 Mb and encodes 1,782 predicted protein-coding genes. In the present study, a comprehensive proteomic profiling was carried out to identify and characterize proteins expressed by B. bifidum S17. A total of 1148 proteins entries were identified by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), representing 64.4% of the predicted proteome. 719 proteins could be assigned to functional categories according to cluster of orthologous groups of proteins (COGs). The COG distribution of the detected proteins highly correlates with that of the complete predicted proteome suggesting a good coverage and representation of the genomic content of B. bifidum S17 by the proteome. COGs that were highly present in the proteome of B. bifidum S17 were Translation, Amino Acid Transport and Metabolism, and Carbohydrate Transport and Metabolism. Complete sets of enzymes for both the bifidus shunt and the Embden-Meyerh of pathway were identified. Further bioinformatic analysis yielded 28 proteins with a predicted extracellular localization including 14 proteins with an LPxTG-motif for cell wall anchoring and two proteins (elongation factor Tu and enolase) with a potential moonlighting function in adhesion. Amongst the predicted extracellular proteins were five of six pilin proteins encoded in the B. bifidum S17 genome as well as several other proteins with a potential role in interaction with host structures. The presented results are the first compilation of a proteomic reference profile for a B. bifidum strain and will facilitate analysis of the molecular mechanisms of physiology, host-interactions and beneficial effects of a potential probiotic strain.