The Type Strain of Bifidobacterium indicum Scardovi and Trovatelli 1969 (Approved Lists 1980) is ATCC 25912, not DSM 20214, and Rejection to Reclassify Bifidobacterium coryneforme as Bifidobacterium indicum.

In 2018, Nouioui et al. proposed that Bifidobacterium coryneforme was a later synonym of Bifidobacterium indicum on the basis of the digital DNA-DNA hybridization (dDDH) value (85.0%) between B. coryneforme LMG 18911T and B. indicum LMG 11587T. However, in the study of Scardovi et al. (1970), the type strains of B. indicum and B. coryneforme only exhibited 60% DNA-DNA hybridization value. In the present study, the genomes of B. coryneforme CGMCC 1.2279T, B. coryneforme JCM 5819T, B. indicum JCM 1302T, B. indicum CGMCC 1.2275T, B. indicum DSM 20214T, B. indicum LMG 27437T, B. indicum ATCC 25912T, B. indicum KCTC 3230T, B. indicum CCUG 34985T, were sequenced, and the taxonomic relationship between B. coryneforme and B. indicum was re-evaluated. On the basis of the results presented here, (i) ATCC 25912 and DSM 20214 deposited by Vittorio Scardovi are two different strains; (ii) the type strain of B. indicum is ATCC 25912T (= JCM 1302T = LMG 27437T = CGMCC 1.2275T = KCTC 3230T), and not DSM 20214 (= BCRC 14674 = CCUG 34985 = LMG 11587); (iii) B. coryneforme and B. indicum represent two different species of the genus Bifidobacterium; (iv) strain DSM 20214 (= BCRC 14674 = CCUG 34985 = LMG 11587) belongs to B. coryneforme.

Bifidobacterium apis sp. nov., isolated from the gut of honeybee (Apis mellifera).

A novel bifidobacterium (designated F753-1T) was isolated from the gut of honeybee (Apis mellifera). Strain F753-1T was characterized using a polyphasic taxonomic approach. Strain F753-1T was phylogenetically related to the type strains of Bifidobacterium mizhiensis, Bifidobacterium asteroides, Bifidobacterium choladohabitans, Bifidobacterium mellis, Bifidobacterium apousia and Bifidobacterium polysaccharolyticum, having 98.4-99.8 % 16S rRNA gene sequence similarities. The phylogenomic tree indicated that strain F753-1T was most closely related to the type strains of B. mellis and B. choladohabitans. Strain F753-1T had the highest average nucleotide identity (94.1-94.5 %) and digital DNA-DNA hybridization (56.3 %) values with B. mellis Bin7NT. Acid production from amygdalin, d-fructose, gentiobiose, d-mannose, maltose, sucrose and d-xylose, activity of α-galactosidase, pyruvate utilization and hydrolysis of hippurate could differentiate strain F753-1T from B. mellis CCUG 66113T and B. choladohabitans JCM 34586T. Based upon the data obtained in the present study, a novel species, Bifidobacterium apis sp. nov., is proposed, and the type strain is F753-1T (=CCTCC AB 2023227T=JCM 36562T=LMG 33388T).

Transplanting human infant gut microbiome species into Galleria mellonella.

OBJECTIVE: Study of the human infant gut microbiome requires the use of surrogate mammalian species such as mice. We sought to investigate the usefulness of the greater wax moth larva, Galleria mellonella, as an alternative. RESULTS: We have analysed the native gut microbiome of Galleria and developed methods for clearing the native microbiome and introducing species from human infant faecal samples. We find that some species, e.g. enterococci, are more successful at recolonisation, but that others, e.g. Bifidobacterium, are less so. The work paves the way for using Galleria rather than mice in this and similar work.

Effects of early-life antibiotics on the developing infant gut microbiome and resistome: a randomized trial.

Broad-spectrum antibiotics for suspected early-onset neonatal sepsis (sEONS) may have pronounced effects on gut microbiome development and selection of antimicrobial resistance when administered in the first week of life, during the assembly phase of the neonatal microbiome. Here, 147 infants born at ≥36 weeks of gestational age, requiring broad-spectrum antibiotics for treatment of sEONS in their first week of life were randomized 1:1:1 to receive three commonly prescribed intravenous antibiotic combinations, namely penicillin + gentamicin, co-amoxiclav + gentamicin or amoxicillin + cefotaxime (ZEBRA study, Trial Register NL4882). Average antibiotic treatment duration was 48 hours. A subset of 80 non-antibiotic treated infants from a healthy birth cohort served as controls (MUIS study, Trial Register NL3821). Rectal swabs and/or faeces were collected before and immediately after treatment, and at 1, 4 and 12 months of life. Microbiota were characterized by 16S rRNA-based sequencing and a panel of 31 antimicrobial resistance genes was tested using targeted qPCR. Confirmatory shotgun metagenomic sequencing was executed on a subset of samples. The overall gut microbial community composition and antimicrobial resistance gene profile majorly shift directly following treatment (R2 = 9.5%, adjusted p-value = 0.001 and R2 = 7.5%, adjusted p-value = 0.001, respectively) and normalize over 12 months (R2 = 1.1%, adjusted p-value = 0.03 and R2 = 0.6%, adjusted p-value = 0.23, respectively). We find a decreased abundance of Bifidobacterium spp. and increased abundance of Klebsiella and Enterococcus spp. in the antibiotic treated infants compared to controls. Amoxicillin + cefotaxime shows the largest effects on both microbial community composition and antimicrobial resistance gene profile, whereas penicillin + gentamicin exhibits the least effects. These data suggest that the choice of empirical antibiotics is relevant for adverse ecological side-effects.

Effect of an infant formula containing sn-2 palmitate on fecal microbiota and metabolome profiles of healthy term infants: a randomized, double-blind, parallel, controlled study.

Different infant diets have strong effects on child development and may engender variations in fecal microbiota and metabolites. The objective of this study was to evaluate the effect of an infant formula containing sn-2 palmitate on fecal microbiota and metabolites in healthy term infants. The study involved three groups as indicated below. Investigational: the group fed a formula containing high sn-2 palmitate for 16 weeks. Control: the group fed a formula using a regular vegetable oil for 16 weeks. Breastfed: the group fed breast milk for 16 weeks. Fecal samples were collected at 8 weeks (n = 35, 37, and 35, respectively) and 16 weeks (n = 30, 32, and 30, respectively) for the control, investigational, and breastfed infants. Microbiota data were obtained using 16S rRNA sequencing. Short-chain fatty acid (SCFA) analysis was performed using GC-MS, and untargeted metabolomics was conducted using LC-MS. The effect of the formula containing sn-2 palmitate was different from that of the control formula on microbiota and metabolites. Sn-2 palmitate promoted the proliferation of Bifidobacterium and reduced the abundance of Escherichia-Shigella at 8 weeks. Furthermore, it increased α-diversity and enhanced acetate content in feces at both 8 and 16 weeks. In the investigational group infants, the abundance of DL-tryptophan, indole-3-acrylic acid, acetyl-ß-methylcholine, L-methionine, and 2-hydroxyvaleric acid significantly increased at 8 weeks, while a notable increase in the abundance of 3-phenyllactic acid, palmitic acid, L-phenylalanine, and leucylproline was observed at 16 weeks. In addition, compared with that of the control infants, the intestinal microbiota and metabolites of sn-2 palmitate-supplemented infants were more similar to those of the breastfed infants. The study hopes to provide a scientific basis for the development of functional infant formulas in the future.

Intestinal microbiota profiles in a genetic model of colon tumorigenesis correlates with colon cancer biomarkers.

Faecal (FM) and colon mucosal associated microbiota (MAM) were studied in a model of colorectal cancer (CRC), the Apc-mutated Pirc rats, and in age-paired wt F344 rats. Principal Coordinates Analysis indicated that samples' distribution was driven by age, with samples of young rats (1 month old; without tumours) separated from older ones (11-month-old; bearing tumours). Diversity analysis showed significant differences between FM and MAM in older Pirc rats, and between MAM of both Pirc and wt rats and the tumour microbiota, enriched in Enterococcus, Escherichia/Shigella, Proteus and Bifidobacteriaceae. In young animals, Pirc FM was enriched in the genus Delftia, while wt FM was enriched in Lactobacillus and Streptococcus. Some CRC biomarkers and faecal short chain fatty acids (SCFAs) were also measured. Colon proliferation and DClK1 expression, a pro-survival mucosal marker, were higher in Pirc than in wt rats, while the mucin MUC2, was lower in Pirc rats. Branched SCFAs were higher in Pirc than in wt animals. By Spearman analysis CRC biomarkers correlated with FM (in both young and old rats) and with MAM (in young rats), suggesting a specific relationship between the gut microbiota profile and these functional mucosal parameters deserving further investigation.

Therapeutic Potential of a Novel Bifidobacterium Identified Through Microbiome Profiling of RA Patients With Different RF Levels.

The potential therapeutic effects of probiotic bacteria in rheumatoid arthritis (RA) remain controversial. Thus, this study aimed to discover potential therapeutic bacteria based on the relationship between the gut microbiome and rheumatoid factor (RF) in RA. Bacterial genomic DNA was extracted from the fecal samples of 93 RA patients and 16 healthy subjects. Microbiota profiling was conducted through 16S rRNA sequencing and bioinformatics analyses. The effects of Bifidobacterium strains on human peripheral blood mononuclear cells and collagen-induced arthritis (CIA) mice were assessed. Significant differences in gut microbiota composition were observed in patients with different RF levels. The relative abundance of Bifidobacterium and Collinsella was lower in RF-high than in RF-low and RF-negative RA patients, while the relative abundance of Clostridium of Ruminococcaceae family was higher in RF-high than in RF-low and RF-negative patients. Among 10 differentially abundant Bifidobacterium, B. longum RAPO exhibited the strongest ability to inhibit IL-17 secretion. Oral administration of B. longum RAPO in CIA mice, obese CIA, and humanized avatar model significantly reduced RA incidence, arthritis score, inflammation, bone damage, cartilage damage, Th17 cells, and inflammatory cytokine secretion. Additionally, B. longum RAPO significantly inhibited Th17 cells and Th17-related genes-IL-17A, IRF4, RORC, IL-21, and IL-23R-in the PBMCs of rheumatoid arthritis patients. Our findings suggest that B. longum RAPO may alleviate RA by inhibiting the production of IL-17 and other proinflammatory mediators. The safety and efficacy of B. longum RAPO in patients with RA and other autoimmune disorders merit further investigation.

Multivariate associative patterns between the gut microbiota and large-scale brain network connectivity.

Research on the gut-brain axis has accelerated substantially over the course of the last years. Many reviews have outlined the important implications of understanding the relation of the gut microbiota with human brain function and behavior. One substantial drawback in integrating gut microbiome and brain data is the lack of integrative multivariate approaches that enable capturing variance in both modalities simultaneously. To address this issue, we applied a linked independent component analysis (LICA) to microbiota and brain connectivity data.We analyzed data from 58 healthy females (mean age = â€¯21.5 years). Magnetic Resonance Imaging data were acquired using resting state functional imaging data. The assessment of gut microbial composition from feces was based on sequencing of the V4 16S rRNA gene region. We used the LICA model to simultaneously factorize the subjects' large-scale brain networks and microbiome relative abundance data into 10 independent components of spatial and abundance variation.LICA decomposition resulted in four components with non-marginal contribution of the microbiota data. The default mode network featured strongly in three components, whereas the two-lateralized fronto-parietal attention networks contributed to one component. The executive-control (with the default mode) network was associated to another component. We found that the abundance of Prevotella genus was associated with the strength of expression of all networks, whereas Bifidobacterium was associated with the default mode and frontoparietal-attention networks.We provide the first exploratory evidence for multivariate associative patterns between the gut microbiota and brain network connectivity in healthy humans considering the complexity of both systems.

Characterization of Bifidobacterium apousia sp. nov., Bifidobacterium choladohabitans sp. nov., and Bifidobacterium polysaccharolyticum sp. nov., three novel species of the genus Bifidobacterium from honey bee gut.

Bifidobacterium is one of the dominating bacterial genera in the honey bee gut, and they are the key degrader of diet polysaccharides for the host. Previous genomic analysis shows that they belong to separate phylogenetic clusters and exhibited different functional potentials in hemicellulose digestion. Here, three novel strains from the genus Bifidobacterium were isolated from the guts of the honey bee (Apis mellifera). Phylogenomic analysis showed that the isolates could be grouped into four phylogenetic clusters. The average nucleotide identity values between strains from different clusters are <95%, while strains in Cluster IV belong to the characterized species Bifidobacterium asteroides. Carbohydrate-active enzyme annotation confirmed that the metabolic capacity for carbohydrates varied between clusters of strains. Cells are Gram-positive rods; they grew both anaerobically and in a CO2-enriched atmosphere. All strains grew at a temperature range of 20-42 °C, with optimum growth at 35 °C. The pH range for growth was 5-9. Strains from different phylogenetic clusters varied in multiple phenotypic and chemotaxonomic characterizations. Thus, we propose three novel species Bifidobacterium apousia sp. nov. whose type strain is W8102T (=CGMCC 1.18893 T = JCM 34587 T), Bifidobacterium choladohabitans sp. nov., whose type strain is B14384H11T (=CGMCC 1.18892 T = JCM 34586 T), and Bifidobacterium polysaccharolyticum sp. nov. whose type strain is W8117T (=CGMCC 1.18894 T = JCM 34588 T).

Isolation and Identification of Lactic Acid Bacteria from Cow Milk and Milk Products.

Lactic acid bacteria (LAB) have long been consumed by people in several fermented foods such as dairy products. A study was conducted on lactating dairy cows to isolate and characterize LAB from dairy products found in and around Bahir-Dar city, North Western Ethiopia. Milk and milk products were randomly collected from dairy farms, milk vending shops, individual households, and supermarkets for bacteriological investigations. A total of sixteen samples were taken from different sources and cultured on different selective media: de Man, Rogosa, and Sharpe (MRS) agar for Lactobacillus spp.; M17 agar for Lactococcus spp.; Rogasa SL agar for Streptococci spp.; and MRS supplemented with cysteine (0.5%) for Bifidobacteria spp. Different laboratory techniques were implemented for LAB isolation and identification. A total of 41 bacterial isolates were grouped under five different genera of LAB and Bifidobacteria spp. were identified based on the growth morphology on the selective media, growth at a different temperature, gas production from glucose, carbohydrate fermentation, and other biochemical tests. LAB genera such as Lactobacillus, Lactococcus, Leuconostoc, Pediococcus, Streptococcus, and Bifidobacterium spp. were isolated and identified from raw milk, cheese, and yogurt. Based on the current study, the majority of the LAB (24.38%) was isolated from cheese and yogurt. Among these, Lactobacillus, Lactococcus (21.94%), Streptococcus (19.51%), Leuconostoc (14.64%), Bifidobacteria (12.19%), and Pediococcus (7.31%) spp. were also identified from these products. Furthermore, based on the bacterial load count and different identification methodologies, our study revealed that Lactobacillus spp. were the dominant LAB isolated from milk and milk products. As a result, since there are few studies on the isolation and identification of lactic acid bacteria from dairy products in Ethiopia, more research studies are needed to complete the identification and characterization to species level and their possible role as probiotics.

The Sulfur Microbial Diet and Risk of Colorectal Cancer by Molecular Subtypes and Intratumoral Microbial Species in Adult Men.

INTRODUCTION: We recently described the sulfur microbial diet, a pattern of intake associated with increased gut sulfur-metabolizing bacteria and incidence of distal colorectal cancer (CRC). We assessed whether this risk differed by CRC molecular subtypes or presence of intratumoral microbes involved in CRC pathogenesis (Fusobacterium nucleatum and Bifidobacterium spp.). METHODS: We performed Cox proportional hazards modeling to examine the association between the sulfur microbial diet and incidence of overall and distal CRC by molecular and microbial subtype in the Health Professionals Follow-Up Study (1986-2012). RESULTS: We documented 1,264 incident CRC cases among 48,246 men, approximately 40% of whom had available tissue data. After accounting for multiple hypothesis testing, the relationship between the sulfur microbial diet and CRC incidence did not differ by subtype. However, there was a suggestion of an association by prostaglandin synthase 2 (PTGS2) status with a multivariable adjusted hazard ratio for highest vs lowest tertile of sulfur microbial diet scores of 1.31 (95% confidence interval: 0.99-1.74, Ptrend = 0.07, Pheterogeneity = 0.04) for PTGS2-high CRC. The association of the sulfur microbial diet with distal CRC seemed to differ by the presence of intratumoral Bifidobacterium spp. with an adjusted hazard ratio for highest vs lowest tertile of sulfur microbial diet scores of 1.65 (95% confidence interval: 1.14-2.39, Ptrend = 0.01, Pheterogeneity = 0.03) for Bifidobacterium-negative distal CRC. We observed no apparent heterogeneity by other tested molecular markers. DISCUSSION: Greater long-term adherence to the sulfur microbial diet could be associated with PTGS2-high and Bifidobacterium-negative distal CRC in men. Additional studies are needed to further characterize the role of gut microbial sulfur metabolism and CRC.

The bifidobacterial distribution in the microbiome of captive primates reflects parvorder and feed specialization of the host.

Bifidobacteria, which commonly inhabit the primate gut, are beneficial contributors to host wellbeing. Anatomical differences and natural habitat allow an arrangement of primates into two main parvorders; New World monkeys (NWM) and Old World monkeys (OWM). The number of newly described bifidobacterial species is clearly elevated in NWM. This corresponds to our finding that bifidobacteria were the dominant group of cultivated gut anaerobes in NWM, while their numbers halved in OWM and were often replaced by Clostridiaceae with sarcina morphology. We examined an extended MALDI-TOF MS database as a potential identification tool for rapid screening of bifidobacterial distribution in captive primates. Bifidobacterial isolates of NWM were assigned mainly to species of primate origin, while OWM possessed typically multi-host bifidobacteria. Moreover, bifidobacterial counts reflected the feed specialization of captive primates decreasing from frugivore-insectivores, gummivore-insectivores, frugivore-folivores to frugivore-omnivores. Amplicon sequencing analysis supported this trend with regards to the inverse ratio of Actinobacteria and Firmicutes. In addition, a significantly higher diversity of the bacterial population in OWM was found. The evolution specialization of primates seems to be responsible for Bifidobacterium abundance and species occurrence. Balanced microbiota of captive primates could be supported by optimized prebiotic and probiotic stimulation based on the primate host.

Effect of probiotics on diversity and function of gut microbiota in Moschus berezovskii.

The forest musk deer, Moschus berezovskii, is a nationally protected species of economic importance in China. However, in captive breeding programmes, they usually die as a result of diarrhoea. In this study, six M. berezovskii were randomly selected and divided into two groups: probiotics group (n = 3) and placebo (control) group (n = 3). The two groups were fed a basal diet that included 2 g probiotics (probiotic group) or 2 g whey powder (placebo group) for 30 days. Faecal samples were collected at day 0, 15 and 30 and evaluated for microbial diversity, species richness and metabolic function. Probiotic intervention significantly improved gut health in M. berezovskii by changing the overall community structure of the gut microbiota. Intake of probiotics reduced the relative abundance of pathogenic bacteria such as Escherichia coli and Citrobacter freundii in the intestinal flora and increased the relative abundance of beneficial Bifidobacterium species and other lactic acid bacteria. At the same time, gut microbiota in the probiotics group were involved in regulating degradation of phenylacetic acid and in dTDP-L-rhamnose synthesis; these processes have the potential to enhance immunity in M. berezovskii. This preliminary study revealed the beneficial effects of probiotics on the gut microbiota of M. berezovskii, which the potential to significantly improve the health, wellbeing and economic value of M. berezovskii.

Long-Term Safety and Efficacy of Prebiotic Enriched Infant Formula-A Randomized Controlled Trial.

The present study aims to evaluate the effects of an infant formula supplemented with a mixture of prebiotic short and long chain inulin-type oligosaccharides on health outcomes, safety and tolerance, as well as on fecal microbiota composition during the first year of life. In a prospective, multicenter, randomized, double-blind study, n = 160 healthy term infants under 4 months of age were randomized to receive either an infant formula enriched with 0.8 g/dL of Orafti®Synergy1 or an unsupplemented control formula until the age of 12 months. Growth, fever (>38 °C) and infections were regularly followed up by a pediatrician. Digestive symptoms, stool consistency as well as crying and sleeping patterns were recorded during one week each study month. Fecal microbiota and immunological biomarkers were determined from a subgroup of infants after 2, 6 and 12 months of life. The intention to treat (ITT) population consisted of n = 149 infants. Both formulae were well tolerated. Mean duration of infections was significantly lower in the prebiotic fed infants (p < 0.05). The prebiotic group showed higher Bifidobacterium counts at month 6 (p = 0.006), and higher proportions of Bifidobacterium in relation to total bacteria at month 2 and 6 (p = 0.042 and p = 0.013, respectively). Stools of infants receiving the prebiotic formula were softer (p < 0.05). Orafti®Synergy1 tended to beneficially impact total daily amount of crying (p = 0.0594). Supplementation with inulin-type prebiotic oligosaccharides during the first year of life beneficially modulates the infant gut microbiota towards higher Bifidobacterium levels at the first 6 months of life, and is associated with reduced duration of infections.

Differences in microbiota between acute and chronic perianal eczema.

ABSTRACT: Microbiota has been suggested to play a role in patients with intestinal and cutaneous diseases. However, the profiling of perianal eczema microbiota has not been described. We have explored the general profile and possible differences between acute and chronic perianal eczema. A total of 101 acute perianal eczema (APE) and 156 chronic perianal eczema (CPE) patients were enrolled in this study and the perianal microbiota was profiled via Illumina sequencing of the 16S rRNA V4 region.The microbial α-diversity and structure are similar in APE and CPE patients; however, the perianal microbiota of the APE patients had a higher content of Staphylococcus (22.2%, P < .01) than that of CPE patients. Top10 genera accounting for more than 60% (68.81% for APE and 65.47% for CPE) of the whole microbiota, including Prevotella, Streptococcus, and Bifidobacterium, show an upregulation trend in the case of APE without reaching statistically significant differences. This study compared the microbiota profiles of acute and chronic perianal eczema. Our results suggest that the microbiota of acute perianal eczema patients is enriched in Staphylococcus compared with that in the chronic group. Our findings provide data for further studies.

Administration of ß-lactam antibiotics and delivery method correlate with intestinal abundances of Bifidobacteria and Bacteroides in early infancy, in Japan.

The intestinal microbiome changes dynamically in early infancy. Colonisation by Bifidobacterium and Bacteroides and development of intestinal immunity is interconnected. We performed a prospective observational cohort study to determine the influence of antibiotics taken by the mother immediately before delivery on the intestinal microbiome of 130 healthy Japanese infants. Faecal samples (383) were collected at 1, 3, and 6 months and analysed using next-generation sequencing. Cefazolin was administered before caesarean sections, whereas ampicillin was administered in cases with premature rupture of the membranes and in Group B Streptococcus-positive cases. Bifidobacterium and Bacteroides were dominant (60-70% mean combined occupancy) at all ages. A low abundance of Bifidobacterium was observed in infants exposed to antibiotics at delivery and at 1 and 3 months, with no difference between delivery methods. A lower abundance of Bacteroides was observed after caesarean section than vaginal delivery, irrespective of antibiotic exposure. Additionally, occupancy by Bifidobacterium at 1 and 3 months and by Bacteroides at 3 months differed between infants with and without siblings. All these differences disappeared at 6 months. Infants exposed to intrapartum antibiotics displayed altered Bifidobacterium abundance, whereas abundance of Bacteroides was largely associated with the delivery method. Existence of siblings also significantly influenced the microbiota composition of infants.

Methods for Isolation and Recovery of Bifidobacteria.

Since their discovery, bifidobacteria have been considered to represent cornerstone commensal microorganisms in the host-microbiome interface at the intestinal level. Bifidobacteria have therefore enjoyed increasing scientific and commercial interest as a source of microorganisms with probiotic potential. However, since functional and probiotic traits are strictly strain-dependent, there is a constant need to isolate, cultivate, and characterize novel strains, activities that require the utilization of appropriate media, as well as robust isolation, cultivation, and preservation techniques. Besides, effective isolation of bifidobacteria from natural environments might require different manipulation and cultivation media and conditions depending on the specific characteristics of the sample material, the presence of competitive microbiota, the metabolic state in which bifidobacteria might be encountered within the sample and the particular metabolic traits of the bifidobacterial species adapted to such inhabitation.A wide array of culture media recipes have been described in the literature to routinely isolate and grow bifidobacteria under laboratory conditions. However, there is not a single and universally applicable medium for effective isolation, recovery, and cultivation of bifidobacteria, as each growth medium has its own particular advantages and limitations. Besides, the vast majority of these media formulations was not specifically formulated for these microorganisms, and thus information on bifidobacterial cultivation options is scarce while being scattered throughout literature. This chapter intends to serve as a resource summarizing the options to cultivate bifidobacteria that have been described to date, highlighting the main advantages and limitations of each of them.

Protocol to Select Bifidobacteria from Fecal and Environmental Samples.

Bifidobacteria are commensal microorganisms able to colonize several ecological niches. Since their discovery, culture-dependent methods combined with the most modern next-generation sequencing techniques have contributed to shed light on the ecological, functional and genomic features of bifidobacteria, purporting them as microorganisms with probiotic traits. Thanks to their acclaimed health-promoting effects, several members of the Bifidobacterium genus have been included in a variety of functional foods and drugs. In this context, the functional relevance of bifidobacteria in the gut explains ongoing efforts to isolate novel and potentially beneficial strains. For this purpose, development of effective and selective isolation protocols in concert with knowledge on the physiological characteristics of bifidobacterial are fundamental requirements for their recovery and discovery from their natural environments, in particular from fecal samples.

Identification of Bifidobacteria by the Phosphoketolase Assay.

Bifidobacteria are commensal bacteria, which naturally colonize the gastrointestinal tract of a large number of animals, including humans, contributing to their health and well-being. An important taxonomic marker for the identification of members of the bifidobacterial group is the presence of the fructose-6-phosphate phosphoketolase (F6PPK) activity. The F6PPK enzyme is involved in the bifidus shunt based on the ability of F6PPK to split fructose-6-phosphate into erythrose-4-phosphate and acetyl phosphate. Here, we describe the two main methods utilized to detect the presence of F6PPK activity, that is, the enzymatic assay and the presence of the D-xylulose-5-phosphate/fructose-6-phosphate phosphoketolase bifidobacterial gene.

Growth stimulation of Bifidobacterium from human colon using daikenchuto in an in vitro model of human intestinal microbiota.

Daikenchuto (DKT) is a Japanese traditional herbal (Kampo) medicine containing ginseng, processed ginger, and Japanese or Chinese pepper. We aimed to determine how DKT affects human colonic microbiota. An in vitro microbiota model was established using fecal inocula collected from nine healthy volunteers, and each model was found to retain operational taxonomic units similar to the ones in the original human fecal samples. DKT was added to the in vitro microbiota model culture at a concentration of 0.5% by weight. Next-generation sequencing of bacterial 16S rRNA gene revealed a significant increase in the relative abundance of bacteria related to the Bifidobacterium genus in the model after incubation with DKT. In pure cultures, DKT significantly promoted the growth of Bifidobacterium adolescentis, but not that of Fusobacterium nucleatum or Escherichia coli. Additionally, in pure cultures, B. adolescentis transformed ginsenoside Rc to Rd, which was then probably utilized for its growth. Our study reveals the in vitro bifidogenic effect of DKT that likely contributes to its beneficial effects on the human colon.