Rapid identification, differentiation, and proposed new taxonomic classification of Bifidobacterium lactis

The Effects of Probiotic Supplementation on Anthropometric Growth and Gut Microbiota Composition in Patients With Prader-Willi Syndrome: A Randomized Double-Blinded Placebo-Controlled Trial

Background: Prader-Willi Syndrome (PWS) is a rare genetic disorder associated with developmental delay, obesity, and neuropsychiatric comorbidities. Bifidobacterium animalis subsp. lactis has demonstrated anti-obesity and anti-inflammatory effects in previous studies.

Aim: To evaluate the effects of Bifidobacterium animalis subsp. lactis probiotics supplementation on anthropometric growth, behavioral symptoms, and gut microbiome composition in patients with PWS.

Methods: Ethical Approval was issued by the Internal Review Board (IRB) of the Second Affiliated Hospital of Kunming Medical University (Review-YJ-2016-06). We conducted a 12-week, randomized, double-blind, placebo-controlled trial in 68 patients with Prader-Willi syndrome aged 11 months−16 years (mean = 4.2 years old) who were randomly assigned to receive daily B. lactis-11 probiotics (6 × 10¹⁰ CFUs) or a placebo sachet. Weight, height, ASQ-3, ABC, SRS-2, and CGI-I were compared between the two groups at baseline and at 6 and 12 weeks into treatment. Gut microbiome data were analyzed with the QIIME 2 software package, and functional gene analysis was conducted with PICRUSt-2.

Results: We found a significant increase in height (mean difference = 2.68 cm, P < 0.05) and improvement in CGI-I (P < 0.05) in the probiotics group compared to the placebo group. No significant change in weight or psychological measures were observed. Probiotic treatment altered the microbiome composition to favor weight loss and gut health and increased the abundance of antioxidant production-related genes.

Conclusions: The findings suggest a novel therapeutic potential for Bifidobacterium animalis subsp. lactis probiotics in Prader-Willi syndrome patients, although further investigation is warranted.

Differential structures and enterotype-like clusters of Bifidobacterium responses to probiotic fermented milk consumption across subjects using a Bifidobacterium-target procedure

The health-promoting attributes of bifidobacteria have piqued interest of researchers worldwide. However, scant published studies are available pertinent to bifidobacteria in microbiota/metagenomics datasets due to its intrinsic low abundance and limitations of detection methods. In this work, we designed a procedure to optimize the detection of the bifidobacterial population in complex biological samples with single-molecule real-time sequencing (SMRT) technology, including one primer pair designated as Bif-6 and a Bifidobacterium-specific database. The optimized procedure detected 14 bifidobacterial species/subspecies in ten human stool samples (2024 sequences per sample) and eight breast milk samples (3473 sequences per sample), respectively. Furthermore, by using the optimized procedure of SMRT, we investigated the effect of a 4-week-intervention of probiotic fermented milk (PFM; 200 g/day) on the gut bifidobacteria population of adults. The results showed that consuming PFM changed the structure and enterotype-like clusters of Bifidobacterium. After the consumption of PFM, the level of gut Bifidobacterium animalis increased significantly, replacing several originally dominating taxa in some subjects, including B. catenulatum, B. breve, and B. bifidum. On the other hand, B. adolescentis was, unaffectedly, the representative species in subjects having an original enterotype-like cluster of B. adolescentis. In conclusion, our work designed a procedure for detecting the bifidobacterial population in complex samples. By applying the currently designed procedure, we found that the PFM intervention changed the bifidobacterial enterotype-like cluster of some subjects, and such change was dependent on the basal bifidobacterial population.

Characterization of the phylogenetic diversity of two novel species belonging to the genus Bifidobacterium: Bifidobacterium cebidarum sp. nov. and Bifidobacterium leontopitheci sp. nov

Two Bifidobacterium strains, i.e., 2176B^T and 2177B^T, were isolated from Golden-Headed Lion Tamarin (Leontopithecus chrysomelas) and Goeldi's monkey (Callimico goeldii). Isolates were shown to be Gram-positive, non-motile, non-sporulating, facultative anaerobic and d-fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA sequences, multilocus sequences (including hsp60, rpoB, dnaJ, dnaG and clpC genes) and the core genome revealed that bifidobacterial strains 2176B^T and 2177B^T exhibit close phylogenetic relatedness to Bifidobacterium felsineum DSM 103139^T and Bifidobacterium bifidum LMG 11041^T, respectively. Further genotyping based on the genome sequence of the isolated strains combined with phenotypic analyses, clearly show that these strains are distinct from each of the type strains of the so far recognized Bifidobacterium species. Thus, Bifidobacterium cebidarum sp. nov. (2176B^T=LMG 31469^T=CCUG 73785^T) and Bifidobacterium leontopitheci sp. nov. (2177B^T=LMG 31471^T=CCUG 73786^T are proposed as novel Bifidobacterium species.

Characterization of the phylogenetic diversity of five novel species belonging to the genus Bifidobacterium: Bifidobacterium castoris sp. nov., Bifidobacterium callimiconis sp. nov., Bifidobacterium goeldii sp. nov., Bifidobacterium samirii sp. nov. and Bifidobacterium dolichotidis sp. nov

Five Bifidobacterium strains, i.e. 2020B^T, 2028B^T, 2033B^T, 2034B^T and 2036B^T, were isolated from European beaver (Castor fiber), Goeldi's marmoset (Callimicogoeldii), black-capped squirrel monkey (Saimiriboliviensissubsp. peruviensis) and Patagonian mara (Dolichotispatagonum). All of these isolates were shown to be Gram-positive, facultative anaerobic, d-fructose 6-phosphate phosphoketolase-positive, non-motile and non-sporulating. Phylogenetic analyses based on 16S rRNA gene sequences, multilocus sequences (including hsp60, rpoB, dnaJ, dnaG and clpC genes) and the core genome revealed that bifidobacterial strains 2020B^T, 2028B^T, 2033B^T, 2034B^T and 2036B^T exhibit close phylogenetic relatedness to Bifidobacterium biavatii DSM 23969^T, Bifidobacterium bifidum LMG 11041^T, Bifidobacterium choerinum LMG 10510^T, Bifidobacterium gallicum LMG 11596^T, Bifidobacterium imperatoris LMG 30297^T, Bifidobacterium italicum LMG 30187^T and Bifidobacterium vansinderenii LMG 30126^T, respectively. Further genotyping based on the genome sequence of the isolated strains combined with phenotypic analyses, clearly show that these strains are distinct from each of the type strains of the so far recognized Bifidobacterium species. Thus, Bifidobacterium castoris sp. nov. (2020B^T=LMG 30937^T=CCUG 72816^T), Bifidobacterium callimiconis sp. nov. (2028B^T=LMG 30938^T=CCUG 72814^T), Bifidobacterium samirii sp. nov. (2033B^T=LMG 30940^T=CCUG 72817^T), Bifidobacterium goeldii sp. nov. (2034B^T=LMG 30939^T=CCUG 72815^T) and Bifidobacterium dolichotidis sp. nov. (2036B^T=LMG 30941^T=CCUG 72818^T) are proposed as novel Bifidobacterium species.

Effects of drinking water synbiotic supplementation in laying hens challenged with Salmonella

This experiment was conducted to study the effects of drinking water supplementation of synbiotic product PoultryStar®sol (containing Lactobacillus reuteri, Bifidobacterium animalis, Pediococcus acidilactici, Enterococcus faecium, and fructo-oligosaccharide) in laying hens with and without a Salmonella challenge. A total of 384 one-day-old layer chicks were randomly distributed to the drinking water synbiotic supplementation or control groups. At 14 wk of age, the birds were vaccinated with a Salmonella vaccine, resulting in a 2 (control and synbiotic) X 2 (non-vaccinated and vaccinated) factorial arrangement. At 24 wk of age, half of the birds in the vaccinated groups and all the birds that were not vaccinated were challenged with Salmonella Enterica serotype Enteritidis, resulting in a 3 (vaccinated, challenged, vaccinated+challenged) X 2 (control and synbiotic) factorial arrangment. At 8 d post-Salmonella challenge, synbiotic supplementation decreased (P = 0.04) cecal S. Enteritidis in the challenge group compared to the un-supplemented challenge group. Birds that were supplemented with synbiotic in the vaccine + challenge group had significantly greater cecal B. animalis and P. acidilactici percentage at 10 d post-Salmonella challenge than the birds in the vaccine + challenge group without synbiotic supplementation. At 3 d post-Salmonella challenge, birds that were supplemented with synbiotic in the challenge group had significantly greater cecal L. reuteri percentage than the birds in the challenge group without synbiotic supplementation. At 17 d post-Salmonella challenge, synbiotic supplementation increased bile anti-Salmonella IgA in the challenge group compared to the birds in the challenge group without synbiotic supplementation by 76.0%. At 10 d (P < 0.01) and 30 d (P = 0.05) post-Salmonella challenge, synbiotic supplementation decreased LITAF mRNA expression compared to the un-supplemented groups. At 3 d post-Salmonella challenge, synbiotic supplementation in the vaccine group had longer jejunal villi compared to the vaccine group without synbiotic supplementation. This experiment demonstrated that drinking water supplementation of the synbiotic product evaluated can significantly manipulate immune response and intestinal microbiota of laying hens post-Salmonella challenge to handle the challenge effectively.

Phylogenetic classification of six novel species belonging to the genus Bifidobacterium comprising Bifidobacterium anseris sp. nov., Bifidobacterium criceti sp. nov., Bifidobacterium imperatoris sp. nov., Bifidobacterium italicum sp. nov., Bifidobacterium margollesii sp. nov. and Bifidobacterium parmae sp. nov

Six Bifidobacterium strains, i.e., Goo31D, Ham19E, Rab10A, Tam1G, Uis4E and Uis1B, were isolated from domestic goose (Anser domesticus), European hamster (Cricetus cricetus), European rabbit (Oryctolagus cuniculus), emperor tamarin (Saguinus imperator) and pygmy marmoset (Callithrix pygmaea). Cells are Gram-positive, non-motile, non-sporulating, facultative anaerobic and fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA, ITS-, multilocus- sequences and the core genome revealed that bifidobacterial strains Goo31D, Ham19E, Rab10A, Tam1G, Uis4E and Uis1B exhibit close phylogenetic relatedness with Bifidobacterium choerinum LMG 10510, Bifidobacterium hapali DSM 100202, Bifidobacterium saguini DSM 23967 and Bifidobacterium stellenboschense DSM 23968. Genotyping based on the genome sequence of the isolated strains combined with phenotypic analyses, clearly show that these strains are distinct from each of the type strains of the so far recognized Bifidobacterium species. Thus, Bifidobacterium anseris sp. nov. (Goo31D=LMG 30189^T=CCUG 70960^T), Bifidobacterium criceti sp. nov. (Ham19E=LMG 30188^T=CCUG 70962^T), Bifidobacterium imperatoris sp. nov. (Tam1G=LMG 30297^T=CCUG 70961^T), Bifidobacterium italicum sp. nov. (Rab10A=LMG 30187^T=CCUG 70963^T), Bifidobacterium margollesii sp. nov. (Uis1B=LMG 30296^T=CCUG 70959^T) and Bifidobacterium parmae sp. nov. (Uis4E=LMG 30295^T=CCUG 70964^T) are proposed as novel Bifidobacterium species.

Tracking the Taxonomy of the Genus Bifidobacterium Based on a Phylogenomic Approach

For decades, bacterial taxonomy has been based on in vitro molecular biology techniques and comparison of molecular marker sequences to measure the degree of genetic similarity and deduce phylogenetic relatedness of novel bacterial species to reference microbial taxa. Due to the advent of the genomic era, access to complete bacterial genome contents has become easier, thereby presenting the opportunity to precisely investigate the overall genetic diversity of microorganisms. Here, we describe a high-accuracy phylogenomic approach to assess the taxonomy of members of the genus Bifidobacterium and identify apparent misclassifications in current bifidobacterial taxonomy. The developed method was validated by the classification of seven novel taxa belonging to the genus Bifidobacterium by employing their overall genetic content. The results of this study demonstrate the potential of this whole-genome approach to become the gold standard for phylogenomics-based taxonomic classification of bacteria.IMPORTANCE Nowadays, next-generation sequencing has given access to genome sequences of the currently known bacterial taxa. The public databases constructed by means of these new technologies allowed comparison of genome sequences between microorganisms, providing information to perform genomic, phylogenomic, and evolutionary analyses. In order to avoid misclassifications in the taxonomy of novel bacterial isolates, new (bifido)bacterial taxons should be validated with a phylogenomic assessment like the approach presented here.

Contemporary nucleic acid-based molecular techniques for detection, identification, and characterization of Bifidobacterium

Bifidobacteria are one of the most important bacterial groups found in the gastrointestinal tract of humans. Medical and food industry researchers have focused on bifidobacteria because of their health-promoting properties. Researchers have historically relied on classic phenotypic approaches (culture and biochemical tests) for detection and identification of bifidobacteria. Those approaches still have values for the identification and detection of some bifidobacterial species, but they are often labor-intensive and time-consuming and can be problematic in differentiating closely related species. Rapid, accurate, and reliable methods for detection, identification, and characterization of bifidobacteria in a mixed bacterial population have become a major challenge. The advent of nucleic acid-based molecular techniques has significantly advanced isolation and detection of bifidobacteria. Diverse nucleic acid-based molecular techniques have been employed, including hybridization, target amplification, and fingerprinting. Certain techniques enable the detection, characterization, and identification at genus-, species-, and strains-levels, whereas others allow typing of species or strains of bifidobacteria. In this review, an overview of methodological principle, technique complexity, and application of various nucleic acid-based molecular techniques for detection, identification, and characterization of bifidobacteria is presented. Advantages and limitations of each technique are discussed, and significant findings based on particular techniques are also highlighted.

Bifidobacteria from the gastrointestinal tract of animals: differences and similarities

At present, the genus Bifidobacterium includes 48 species and subspecies, and this number is expected to increase. Bifidobacteria are found in different ecological niches. However, most were originally isolated from animals, mainly mammals, especially during the milk feeding period of life. Their presence in high numbers is associated with good health of the host. Moreover, bifidobacteria are often found in poultry and insects that exhibit a social mode of life (honeybees and bumblebees). This review is designed as a summary of currently known species of the genus Bifidobacterium, especially focused on their difference and similarities. The primary focus is on their occurrence in the digestive tract of animals, as well as the specificities of animal strains, with regard to their potential use as probiotics.

Bifidobacterium animalis subsp. lactis ATCC 27673 is a genomically unique strain within its conserved subspecies

Many strains of Bifidobacterium animalis subsp. lactis are considered health-promoting probiotic microorganisms and are commonly formulated into fermented dairy foods. Analyses of previously sequenced genomes of B. animalis subsp. lactis have revealed little genetic diversity, suggesting that it is a monomorphic subspecies. However, during a multilocus sequence typing survey of Bifidobacterium, it was revealed that B. animalis subsp. lactis ATCC 27673 gave a profile distinct from that of the other strains of the subspecies. As part of an ongoing study designed to understand the genetic diversity of this subspecies, the genome of this strain was sequenced and compared to other sequenced genomes of B. animalis subsp. lactis and B. animalis subsp. animalis. The complete genome of ATCC 27673 was 1,963,012 bp, contained 1,616 genes and 4 rRNA operons, and had a G+C content of 61.55%. Comparative analyses revealed that the genome of ATCC 27673 contained six distinct genomic islands encoding 83 open reading frames not found in other strains of the same subspecies. In four islands, either phage or mobile genetic elements were identified. In island 6, a novel clustered regularly interspaced short palindromic repeat (CRISPR) locus which contained 81 unique spacers was identified. This type I-E CRISPR-cas system differs from the type I-C systems previously identified in this subspecies, representing the first identification of a different system in B. animalis subsp. lactis. This study revealed that ATCC 27673 is a strain of B. animalis subsp. lactis with novel genetic content and suggests that the lack of genetic variability observed is likely due to the repeated sequencing of a limited number of widely distributed commercial strains.

Exploration of the genomic diversity and core genome of the Bifidobacterium adolescentis phylogenetic group by means of a polyphasic approach

In the current work, we describe genome diversity and core genome sequences among representatives of three bifidobacterial species, i.e., Bifidobacterium adolescentis, Bifidobacterium catenulatum, and Bifidobacterium pseudocatenulatum, by employing a polyphasic approach involving analysis of 16S rRNA gene and 16S-23S internal transcribed spacer (ITS) sequences, pulsed-field gel electrophoresis (PFGE), and comparative genomic hybridization (CGH) assays.

Short communication: the complete genome sequence of Bifidobacterium animalis subspecies animalis ATCC 25527(T) and comparative analysis of growth in milk with B. animalis subspecies lactis DSM 10140(T)

The objective of this work was to sequence the genome of Bifidobacterium animalis ssp. animalis ATCC 25527(T), the subspecies most closely related to B. animalis ssp. lactis, some strains of which are widely added to dairy foods as probiotics. The complete 1,932,963-bp genome was determined by a combination of 454-shotgun sequencing and PCR gap closing, and the completed assembly was verified by comparison with a KpnI optical map. Comparative analysis of the B. animalis ssp. animalis ATCC 25527(T) and B. animalis ssp. lactis DSM 10140(T) genomes revealed high degrees of synteny and sequence homology. Comparative genomic analysis revealed 156 and 182 genes that were unique to and absent in the B. animalis ssp. animalis genome, respectively. Among these was a set of unique clustered regularly interspaced short palindromic repeats (CRISPR)-associated genes and a novel CRISPR locus containing 30 spacers in the genome of B. animalis ssp. animalis. Although previous researchers have suggested that one of the defining phenotypic differences between B. animalis ssp. animalis and B. animalis ssp. lactis is the ability of the latter to grow in milk and milk-based media, the differential gene content did not provide insights to explain these differences. Furthermore, growth and acid production in milk and milk-based media did not differ significantly between B. animalis ssp. lactis (DSM 10140(T) and Bl04) and B. animalis ssp. animalis (ATCC 25527(T)). Growth of these strains in supplemented milk suggested that growth was limited by a lack of available low-molecular-weight nitrogen in the 3 strains examined.

Bifidobacterium animalis subsp. lactis BB-12 administration in early childhood: a randomized clinical trial of effects on oral colonization by mutans streptococci and the probiotic

A randomized clinical trial studied the effects of early administration of Bifidobacterium animalis subsp. lactis BB-12 (BB-12) on oral colonization of (1) mutans streptococci (MS), and (2) BB-12. In this double-blind, placebo-controlled study, infants (n = 106) received probiotic bacteria (BB-12 group), xylitol (X group), or sorbitol (S group). Test tablets were administered twice a day (from the age of 1-2 months) with a novel slow-release pacifier or a spoon (daily dose of BB-12 10(10) CFU, polyol 200-600 mg). Samples were collected from mucosa/teeth at the age of 8 months and 2 years for BB- 12 determination (qPCR) and plate culturing of MS (MSB, TYCSB), lactobacilli (Rogosa) and yeasts (Sabouraud). The MS levels of the mothers were determined (Dentocult SM Strip Mutans). The baseline characteristics of the three groups were similar. Mean duration of tablet delivery was 14.9 ± 6.7 months. In all groups, >90% of the mothers showed high MS counts (log CFU ≥5). MS colonization percentages of the children at the age of 2 years were rather low (BB-12 group: 6%; X group: 31%; S group: 10%; p < 0.05). The levels of lactobacilli and yeasts did not differ between the groups. BB-12 cell counts barely exceeding the detection limit were found in three of the oral samples of the 8-month-old children; however, the 2-year samples did not contain BB-12. The early administration of BB-12 did not result in permanent oral colonization of this probiotic or significantly affect MS colonization in the children.

Rapid discrimination of Bifidobacterium animalis subspecies by matrix-assisted laser desorption ionization-time of flight mass spectrometry

Currently, the species Bifidobacterium animalis consists of two subspecies, B. animalis subsp. lactis and B. animalis subsp. animalis. Among these two subspecies, B. animalis subsp. lactis is especially important because it is widely used in the manufacture of probiotic dairy products. The application of these microbes in the food industry demands fast, accurate and low cost methods to differentiate between species and strains. Although various genotypic methods have been employed to discriminate between these two subspecies, they are not easily adapted for rapid identification in the industry. The purpose of this study was to evaluate the use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) to differentiate between the two subspecies of B. animalis, and for discrimination at strain level. We identified twenty-three strains of B. animalis at subspecies and strain level by genotypic methods and by proteomics using MALDI-TOF MS. The proteomics identification by MALDI-TOF was nearly identical to that obtained by genotypic identification using comparison of tuf and atpD gene sequences, and single-nucleotide polymorphisms (SNPs), insertions, and deletions (INDELs). We identified four protein markers, L1, L2, A1, and A2, which are useful for discriminating between both subspecies. Proteomics identification using MALDI-TOF MS was therefore an accurate method for discriminating and identifying these bacteria. Given the speed in which this method is achieved (~20 min including sample preparation), MALDI-TOF MS is promising as a tool for rapid discrimination of starter cultures and probiotics.

Progress in genomics, metabolism and biotechnology of bifidobacteria

Members of the genus Bifidobacterium were first described over a century ago and were quickly associated with a healthy intestinal tract due to their numerical dominance in breast-fed babies as compared to bottle-fed infants. Health benefits elicited by bifidobacteria to its host, as supported by clinical trials, have led to their wide application as probiotic components of health-promoting foods, especially in fermented dairy products. However, the relative paucity of genetic tools available for bifidobacteria has impeded development of a comprehensive molecular understanding of this genus. In this review we present a summary of current knowledge on bifidobacterial metabolism, classification, physiology and genetics and outline the currently available methods for genetically accessing and manipulating the genus.

Genomic insights into bifidobacteria

Since the discovery in 1899 of bifidobacteria as numerically dominant microbes in the feces of breast-fed infants, there have been numerous studies addressing their role in modulating gut microflora as well as their other potential health benefits. Because of this, they are frequently incorporated into foods as probiotic cultures. An understanding of their full interactions with intestinal microbes and the host is needed to scientifically validate any health benefits they may afford. Recently, the genome sequences of nine strains representing four species of Bifidobacterium became available. A comparative genome analysis of these genomes reveals a likely efficient capacity to adapt to their habitats, with B. longum subsp. infantis exhibiting more genomic potential to utilize human milk oligosaccharides, consistent with its habitat in the infant gut. Conversely, B. longum subsp. longum exhibits a higher genomic potential for utilization of plant-derived complex carbohydrates and polyols, consistent with its habitat in an adult gut. An intriguing observation is the loss of much of this genome potential when strains are adapted to pure culture environments, as highlighted by the genomes of B. animalis subsp. lactis strains, which exhibit the least potential for a gut habitat and are believed to have evolved from the B. animalis species during adaptation to dairy fermentation environments.

Isolation and characterisation of an oxygen, acid and bile resistant Bifidobacterium animalis subsp. lactis Qq08

BACKGROUND

Currently, bifidobacteria are recognised as one of the most important bacteria used as probiotics, which promote human health. However, their commercial application has been limited by their anaerobic nature. The purpose of this study was to select an oxygen, acid and bile resistant strain of bifidobacterium for use as a new probiotic.

RESULTS

A total of 10 strains of bifidobacteria from different sources were analysed for their relative bacterial growth ratio (RBGR) in different oxygen concentrations. Three strains with high RBGR values were selected and their survival rates in acid environment and bile salt conditions were investigated in vitro. One strain showed high tolerance to low pH, giving a survival rate of 84% at pH 2 after 4 h incubation, and high tolerance to bile, more than 90% after 4.5 h incubation at 0.01 g mL(-1) bile concentration. This strain was identified as Bifidobacterium animalis subsp. lactis strain Qq08 based on polyphasic taxonomy approaches, such as phenotype analysis and 16S rRNA and 16S to 23S internally transcribed spacer sequence analyses.

CONCLUSION

We isolated an aerotolerant bifidobacterium and identified it as Bifidobacterium animalis subsp. lactis Qq08. This strain has characteristics more favourable than the commercial probiotic strain, Bifidobacterium lactis Bb12.

Antibiotic susceptibility of bifidobacterial strains distributed in the Japanese market

The aim of the present study was to analyze the antibiotic susceptibility of bifidobacterial strains distributed in the Japanese market. A total of 23 strains, including probiotic isolates from foods, supplements, pharmaceuticals and reference strains of each species (or subspecies), were tested for susceptibility to 15 antibiotics by the broth microdilution method and examined for the presence of possible resistant determinants. The strains were susceptible overall to chloramphenicol, ampicillin, vancomycin and linezolid, and were intrinsically resistant to aminoglycoside group agents. Susceptibility to erythromycin, clindamycin, rifampicin, tetracycline and trimethoprim varied among the strains. All strains of Bifidobacterium animalis subsp. lactis were resistant to tetracycline and appeared to harbor tet(W) genes. No risk factor for safety was found for bifidobacterial strains distributed in the Japanese market in respect of their antimicrobial resistance, although the presence of the tet(W) gene in some strains stresses the need for future evaluation.

Species delineation and clonal diversity in four Bifidobacterium species as revealed by multilocus sequencing

The genus Bifidobacterium comprises several species that are important contributors to the gut microbiome, with some strains having beneficial health effects. Understanding the evolutionary emergence of advantageous biological properties requires knowledge of the genetic diversity and clonal structure of species. We sequenced seven housekeeping genes in 119 Bifidobacterium strains of Bifidobacterium animalis, Bifidobacterium bifidum, Bifidobacterium breve and Bifidobacterium longum. Phylogenetic analysis of concatenated sequences delineated sequence clusters that correspond to previously named taxa, and suggested that B. longum subsp. infantis is a nascent lineage emerging from within B. longum subsp. longum. Clear traces of recombination among distant bifidobacterial species indicate leaky species borders and warn against the practice of single gene-based identification. Multilocus sequence typing achieved precise strain genotyping, with discrimination indices above 99% in B. bifidum, B. breve and B. longum, providing a powerful tool for strain traceability, colonization dynamics and ecological studies. Frequent homologous recombination accelerates clonal diversification and may facilitate the transfer of biological properties among bifidobacterial strains.

Strain-specific genotyping of Bifidobacterium animalis subsp. lactis by using single-nucleotide polymorphisms, insertions, and deletions

Several probiotic strains of Bifidobacterium animalis subsp. lactis are widely supplemented into food products and dietary supplements due to their documented health benefits and ability to survive within the mammalian gastrointestinal tract and acidified dairy products. The strain specificity of these characteristics demands techniques with high discriminatory power to differentiate among strains. However, to date, molecular approaches, such as pulsed-field gel electrophoresis and randomly amplified polymorphic DNA-PCR, have been ineffective at achieving strain separation due to the monomorphic nature of this subspecies. Previously, sequencing and comparison of two B. animalis subsp. lactis genomes (DSMZ 10140 and Bl-04) confirmed this high level of sequence similarity, identifying only 47 single-nucleotide polymorphisms (SNPs) and four insertions and/or deletions (INDELs) between them. In this study, we hypothesized that a sequence-based typing method targeting these loci would permit greater discrimination between strains than previously attempted methods. Sequencing 50 of these loci in 24 strains of B. animalis subsp. lactis revealed that a combination of nine SNPs/INDELs could be used to differentiate strains into 14 distinct genotypic groups. In addition, the presence of a nonsynonymous SNP within the gene encoding a putative glucose uptake protein was found to correlate with the ability of certain strains to transport glucose and to grow rapidly in a medium containing glucose as the sole carbon source. The method reported here can be used in clinical, regulatory, and commercial applications requiring identification of B. animalis subsp. lactis at the strain level.

Comparison of the complete genome sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04

Bifidobacteria are important members of the human gut flora, especially in infants. Comparative genomic analysis of two Bifidobacterium animalis subsp. lactis strains revealed evolution by internal deletion of consecutive spacer-repeat units within a novel clustered regularly interspaced short palindromic repeat locus, which represented the largest differential content between the two genomes. Additionally, 47 single nucleotide polymorphisms were identified, consisting primarily of nonsynonymous mutations, indicating positive selection and/or recent divergence. A particular nonsynonymous mutation in a putative glucose transporter was linked to a negative phenotypic effect on the ability of the variant to catabolize glucose, consistent with a modification in the predicted protein transmembrane topology. Comparative genome sequence analysis of three Bifidobacterium species provided a core genome set of 1,117 orthologs complemented by a pan-genome of 2,445 genes. The genome sequences of the intestinal bacterium B. animalis subsp. lactis provide insights into rapid genome evolution and the genetic basis for adaptation to the human gut environment, notably with regard to catabolism of dietary carbohydrates, resistance to bile and acid, and interaction with the intestinal epithelium. The high degree of genome conservation observed between the two strains in terms of size, organization, and sequence is indicative of a genomically monomorphic subspecies and explains the inability to differentiate the strains by standard techniques such as pulsed-field gel electrophoresis.

Exploring the diversity of the bifidobacterial population in the human intestinal tract

Although the health-promoting roles of bifidobacteria are widely accepted, the diversity of bifidobacteria among the human intestinal microbiota is still poorly understood. We performed a census of bifidobacterial populations from human intestinal mucosal and fecal samples by plating them on selective medium, coupled with molecular analysis of selected rRNA gene sequences (16S rRNA gene and internally transcribed spacer [ITS] 16S-23S spacer sequences) of isolated colonies. A total of 900 isolates were collected, of which 704 were shown to belong to bifidobacteria. Analyses showed that the culturable bifidobacterial population from intestinal and fecal samples include six main phylogenetic taxa, i.e., Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bifidobacterium adolescentis, Bifidobacterium pseudolongum, Bifidobacterium breve, and Bifidobacterium bifidum, and two species mostly detected in fecal samples, i.e., Bifidobacterium dentium and Bifidobacterium animalis subp. lactis. Analysis of bifidobacterial distribution based on age of the subject revealed that certain identified bifidobacterial species were exclusively present in the adult human gut microbiota whereas others were found to be widely distributed. We encountered significant intersubject variability and composition differences between fecal and mucosa-adherent bifidobacterial communities. In contrast, a modest diversification of bifidobacterial populations was noticed between different intestinal regions within the same individual (intrasubject variability). Notably, a small number of bifidobacterial isolates were shown to display a wide ecological distribution, thus suggesting that they possess a broad colonization capacity.

Transport of glucose by Bifidobacterium animalis subsp. lactis occurs via facilitated diffusion

Two strains of Bifidobacterium animalis subsp. lactis were indistinguishable by several nucleic acid-based techniques; however, the type strain DSMZ 10140 was glucose utilization positive, while RB 4825, an industrially employed strain, was unable to grow rapidly on glucose as the principal carbon source. This difference was attributed to the presence of a low-affinity facilitated-diffusion glucose transporter identified in DSMZ 10140 but lacking in RB 4825. Uptake of D-[U-(14)C]glucose in DSMZ 10140 was stimulated by monovalent cations (ammonium, sodium, potassium, and lithium) and inhibited by divalent cations (calcium and magnesium). When competitor carbohydrates were included in the uptake assays, stereospecific inhibition was exhibited, with greater competition by methyl-beta-glucoside than methyl-alpha-glucoside. Significant inhibition (>30%) was observed with phloretin, an inhibitor of facilitated diffusion of glucose, whereas there was no inhibition by sodium fluoride, iodoacetate, sodium arsenate, sodium azide, 2,4-dinitrophenol, monensin, or valinomycin, which typically reduce energy-driven transport. Based on kinetic analyses, the mean values for K(t) and V(max) were 14.8 +/- 3.4 mM D-glucose and 0.13 +/- 0.03 micromol glucose/min/mg cell protein, respectively. Glucose uptake by several glucose-utilizing commercial strains of B. animalis subsp. lactis was also inhibited by phloretin, indicating the presence of facilitated diffusion glucose transporters in those strains. Since DSMZ 10140 has been previously reported to lack a functional glucose phosphoenolpyruvate phosphotransferase system, the glucose transporter identified here is responsible for much of the organism's glucose uptake.

Detection of Bifidobacterium animalis subsp. lactis (Bb12) in the intestine after feeding of sows and their piglets

A real-time PCR method has been developed to distinguish Bifidobacterium animalis subspecies in the gastrointestinal tracts of pigs. Identification of a highly conserved single-copy tuf gene encoding the elongation factor Tu involved in bacterial protein biosynthesis was used as a marker to differentiate homologous Bifidobacterium animalis subsp. lactis (strain Bb12) from Bifidobacterium animalis subsp. animalis, as well as Bifidobacterium suis, Bifidobacterium breve, Bifidobacterium longum, several species of Lactobacillus, and Enterococcus faecium. Real-time PCR detection of serially diluted DNA extracted from a pure culture of Bb12 was linear for bacterial numbers ranging from 10 to 10,000 tuf gene copies per PCR (r(2) = 0.99). Relative differences in Bb12 bacterial numbers in pigs fed daily with Bb12 were determined after detection of Bb12 tuf gene copies in DNA extracted from the intestinal contents. Piglets treated with Bb12 immediately after birth maintained a high level of Bb12 in their large intestines with continuous daily administration of Bb12. Piglets born to Bb12-treated sows during the last third of their gestation and also treated with Bb12 at birth (T/T group) had a higher number of Bb12 organisms per gram of intestinal contents compared to placebo-treated piglets born to placebo-treated sows (C/C group), Bb12-treated sows (T/C group), or piglets born to placebo sows but treated with Bb12 immediately after birth (C/T group). In addition, there was a significant increase in gene expression for Toll-like receptor 9 (TLR9) in piglets from the T/T group, with no change in TLR2 and TLR4. These findings suggest that the tuf gene represents a specific and functional marker for detecting Bifidobacterium animalis subsp. lactis strain Bb12 within the microbiota of the intestine.

Evaluation of the PCR method for identification of Bifidobacterium species

AIMS

Bifidobacterium species are known for their beneficial effects on health and their wide use as probiotics. Although various polymerase chain reaction (PCR) methods for the identification of Bifidobacterium species have been published, the reliability of these methods remains open to question.

METHODS AND RESULTS

In this study, we evaluated 37 previously reported PCR primer sets designed to amplify 16S rDNA, 23S rDNA, intergenic spacer regions, or repetitive DNA sequences of various Bifidobacterium species.

CONCLUSIONS

Ten of 37 experimental primer sets showed specificity for B. adolescentis, B. angulatum, B. pseudocatenulatum, B. breve, B. bifidum, B. longum, B. longum biovar infantis and B. dentium.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results suggest that published Bifidobacterium primer sets should be re-evaluated for both reproducibility and specificity for the identification of Bifidobacterium species using PCR. Improvement of existing PCR methods will be needed to facilitate identification of other Bifidobacterium strains, such as B. animalis, B. catenulatum, B. thermophilum and B. subtile.

Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum

Actinobacteria constitute one of the largest phyla among bacteria and represent gram-positive bacteria with a high G+C content in their DNA. This bacterial group includes microorganisms exhibiting a wide spectrum of morphologies, from coccoid to fragmenting hyphal forms, as well as possessing highly variable physiological and metabolic properties. Furthermore, Actinobacteria members have adopted different lifestyles, and can be pathogens (e.g., Corynebacterium, Mycobacterium, Nocardia, Tropheryma, and Propionibacterium), soil inhabitants (Streptomyces), plant commensals (Leifsonia), or gastrointestinal commensals (Bifidobacterium). The divergence of Actinobacteria from other bacteria is ancient, making it impossible to identify the phylogenetically closest bacterial group to Actinobacteria. Genome sequence analysis has revolutionized every aspect of bacterial biology by enhancing the understanding of the genetics, physiology, and evolutionary development of bacteria. Various actinobacterial genomes have been sequenced, revealing a wide genomic heterogeneity probably as a reflection of their biodiversity. This review provides an account of the recent explosion of actinobacterial genomics data and an attempt to place this in a biological and evolutionary context.

Antibiotic resistance of lactic acid bacteria and Bifidobacterium spp. isolated from dairy and pharmaceutical products

The outlines of antibiotic resistance of some probiotic microorganisms were studied. This study was conducted with the double purpose of verifying their ability to survive if they are taken simultaneously with an antibiotic therapy and to increase the selective properties of suitable media for the isolation of samples containing mixed bacterial populations. We isolated from commercial dairy and pharmaceutical products, 34 strains declared as probiotics, belonging to the genera Bifidobacterium and Lactobacillus, and 21 strains of starter culture bacteria. All the microorganisms have been compared by electrophoresis of the soluble proteins for the purpose of identifying them. A Multiplex-PCR with genus- and species-specific primers was used to detect for Bifidobacterium animalis subsp. lactis presence. All bifidobacteria were B. animalis subsp. lactis except one Bifidobacterium longum. Sometimes the identification showed that the used strain was not the one indicated on the label. The lactobacilli were Lactobacillus acidophilus, Lactobacillus casei, and Lactobacillus delbrueckii subsp. bulgaricus. The streptococci were all Streptococcus thermophilus. The minimal inhibitory concentration (MIC) of 24 common antibiotic substances has been valued by the broth microdilution method. All tested strains were susceptible to ampicillin, bacitracin, clindamycin, dicloxacillin, erytromycin, novobiocin, penicillin G, rifampicin (MIC(90) ranging from 0.01 to 4 microg/ml); resistant to aztreonam, cycloserin, kanamycin, nalidixic acid, polymyxin B and spectinomycin (MIC(90) ranging from 64 to >1000 microg/ml). The susceptibility to cephalothin, chloramphenicol, gentamicin, lincomycin, metronidazole, neomycin, paromomycin, streptomycin, tetracycline and vancomycin was variable and depending on the species.

Identification and differentiation of Lactobacillus, Streptococcus and Bifidobacterium species in fermented milk products with bifidobacteria

The aim of this study was to identify and discriminate bacteria contained in commercial fermented milks with bifidobacteria by the use of amplified ribosomal DNA restriction analysis (ARDRA) and randomly amplified polymorphic DNA (RAPD) techniques. ARDRA of the 16S rDNA gene and RAPD were performed on 13 Lactobacillus strains, 13 Streptococcus and 13 Bifidobacterium strains isolated from commercial fermented milk. Lactobacillus delbrueckii, Streptococcus thermophilus and Bifidobacterium animalis isolates were identified by genus- and species-PCR and also, they were differentiated at genus and species level by ARDRA using MwoI restriction enzyme. The ARDRA technique allowed for the discrimination among these three related genus with the use of only one restriction enzyme, since distinctive profiles were obtained for each genus. Therefore it can be a simple, rapid and useful method for routine identification. Also, RAPD technique allowed the discrimination of all bacteria contained in dairy products, at genus- and strain-level by the performance of one PCR reaction.

Genomics as a means to understand bacterial phylogeny and ecological adaptation: the case of bifidobacteria

The field of microbiology has in recent years been transformed by the ever increasing number of publicly available whole-genome sequences. This sequence information has significantly enhanced our understanding of the physiology, genetics and evolutionary development of bacteria. Among the latter group of microorganisms, bifidobacteria represent important human commensals because of their perceived contribution to maintaining a balanced gastrointestinal tract microbiota. In recent years bifidobacteria have drawn much scientific attention because of their use as live bacteria in numerous food preparations with various health-related claims. For this reason, these bacteria constitute a growing area of interest with respect to genomics, molecular biology and genetics. Recent genome sequencing of a number of bifidobacterial species has allowed access to the complete genetic make-up of these bacteria. In this review we will discuss how genomic data has allowed us to understand bifidobacterial evolution, while also revealing genetic functions that explains their presence in the particular ecological environment of the gastrointestinal tract.

The F1F0-ATPase of Bifidobacterium animalis is involved in bile tolerance

Adaptation and tolerance to bile stress are important factors for the survival of bifidobacteria in the intestinal tract. Bifidobacterium animalis is a probiotic microorganism which has been largely applied in fermented dairy foods due to its technological properties and its health-promoting effects for humans. The effect of the presence of bile on the activity and expression of F(1)F(0)-ATPase, the pool of ATP and the intracellular pH of B. animalis IPLA 4549 and its mutant with acquired resistance to bile B. animalis 4549dOx was determined. The bile-resistant mutant tolerated the acid pH better than its parent strain. Bile induced the expression of the F(1)F(0)-ATPase and increased the membrane-bound H(+)-ATPase activity, in both parent and mutant strains. In acidic conditions (pH 5.0), the expression and the activity of this enzyme were higher in the mutant than in the parent strain when cells were grown in the absence of bile. Total ATP content was higher for the mutant in the absence of bile, whereas the presence of bile induced a decrease of intracellular ATP levels, which was much more pronounced for the parent strain. At pH 4.0, and independently on the presence or absence of bile, the mutant showed a higher intracellular pH than its parent strain. These findings suggest that the bile-adapted B. animalis strain is able to tolerate bile by increasing the intracellular ATP reserve, and by inducing proton pumping by the F(1)F(0)-ATPase, therefore tightly regulating the internal pH, and provide a link between the physiological state of the cell and the response to bile.

Technical note: a rapid pulsed-field gel electrophoresis method for analysis of bifidobacteria

Pulsed-field gel electrophoresis (PFGE) is a widely used and highly discriminatory molecular typing method that has been applied to bifidobacteria. However, published PFGE protocols used with bifidobacteria require between 5 and 7 d to complete. A rapid PFGE method was developed that can be completed within 24 h.

The ClgR protein regulates transcription of the clpP operon in Bifidobacterium breve UCC 2003

Five clp genes (clpC, clpB, clpP1, clpP2, and clpX), representing chaperone- and protease-encoding genes, were previously identified in Bifidobacterium breve UCC 2003. In the present study, we characterize the B. breve UCC 2003 clpP locus, which consists of two paralogous genes, designated clpP1 and clpP2, whose deduced protein products display significant similarity to characterized ClpP peptidases. Transcriptional analyses showed that the clpP1 and clpP2 genes are transcribed in response to moderate heat shock as a bicistronic unit with a single promoter. The role of a clgR homologue, known to control the regulation of clpP gene expression in Streptomyces lividans and Corynebacterium glutamicum, was investigated by gel mobility shift assays and DNase I footprint experiments. We show that ClgR, which in its purified form appears to exist as a dimer, requires a proteinaceous cofactor to assist in specific binding to a 30-bp region of the clpP promoter region. In pull-down experiments, a 56-kDa protein copurified with ClgR, providing evidence that the two proteins also interact in vivo and that the copurified protein represents the cofactor required for ClgR activity. The prediction of the ClgR three-dimensional structure provides further insights into the binding mode of this protein to the clpP1 promoter region and highlights the key amino acid residues believed to be involved in the protein-DNA interaction.

A bile salt-resistant derivative of Bifidobacterium animalis has an altered fermentation pattern when grown on glucose and maltose

The growth of Bifidobacterium animalis subsp. lactis IPLA 4549 and its derivative with acquired resistance to bile, B. animalis subsp. lactis 4549dOx, was evaluated in batch cultures with glucose or the glucose disaccharide maltose as the main carbon source. The acquisition of bile salt resistance caused a change in growth pattern for both sugars, which mainly resulted in a preferential use of maltose compared to glucose, whereas the mother strain used both carbohydrates in a similar way. High-performance liquid chromatography and gas chromatography-mass spectrometry analyses were performed to determine the amounts of glucose consumption and organic acid and ethanol formation from glucose by buffered resting cells taken at different points during growth. Resting cells of the bile-adapted strain generally consumed less glucose than those of the nonadapted one but showed an enhanced production of ethanol and higher acetic acid-to-lactic acid as well as formic acid-to-lactic acid ratios. These findings suggest a shift in the catabolism of carbohydrates promoted by the acquisition of bile resistance that may cause changes in the redox potential and improvements in the cellular ATP yield.