Identification and tracing of Bifidobacterium species by use of enterobacterial repetitive intergenic consensus sequences

Transmission of β-lactamases in the pork food chain: A public health concern

Antimicrobial resistance (AMR) is a risk for public health that requires management in a One Health perspective, including humans, animals, and the environment. The food production chain has been identified as a possible route of transmission of AMR bacteria to humans. The most critical issue regards resistance to the Critically Important Antimicrobials (CIAs), such as β-lactams antibiotics. Here, pigs were analysed along the entire food producing chain, including feces, carcasses and pork products (fresh meat, fermented and seasoned products) ensuring treaciability of all samples. Escherichia coli were isolated and their ability to produce ESBL and AmpC β-lactamases was evaluated both phenotypically and genotypically. Strains with the same AMR profile from feces, carcasses, and meat products were selected for phylogenetic and comparative genomic analyses to evaluate the possible "farm-to-fork" transmission of β-lactams resistant bacteria. Results showed that the percentage of ESBL strains in fecal E. coli was approximately 7% and increased slightly in the pork food chain: the 10% of ESBL E. coli isolated from carcasses and the 12.5% of isolates from fresh meat products. AmpC E. coli were found only in feces, carcasses, and fresh meat with a low prevalence. Results showed that of the 243 pigs followed along the entire food chain genetic similarities in E. coli isolated from farm-to-fork were found in only one pig (feces, carcasses and fresh meat). Frequent similarities were shown in resistant E. coli isolates from carcasses and fresh meat or fermented product (three pork food chain). Moreover, in one case, bacteria isolated from fresh meat and fermented product were genotypically similar. Concluding, direct transmission of β-lactams resistance from farm-to-fork is possible but not frequent. Further studies are needed to improve risk communication to consumers and access to clear and reliable information and health concerns on food.

The Pork Food Chain as a Route of Transmission of Antimicrobial Resistant Escherichia coli: A Farm-to-Fork Perspective

Antimicrobial resistance (AMR) is a public health risk that needs to be faced from a One Health perspective that includes humans, animals, and environmental health. The food production chain has been identified as a possible route of transmission of AMR bacteria to humans. The most critical phenomenon is related to Critically Important Antimicrobial (CIA) resistance. β-lactams antibiotics (cephalosporin of 3rd, 4th generation, carbapenem, monobactams, and penicillins), quinolones, aminoglycosides, polymyxin, and glycylcyclines were the CIAs chosen in this study. Samples derived from all the stages of the pork food production chain were collected, including pig feces, carcasses, and pork food products (fresh meat, fermented, and seasoned). Escherichia coli were isolated, and AMR and MDR profiles were evaluated. Enterobacterial Repetitive Intragenic Consensus (ERIC-PCR) was used to evaluate phylogenetic similarities. Data showed that 50% of phenotypical AMR observed in the entire pork food chain were related phylogenetically. The contamination of fresh meat, in half of the cases, was not directly related to contamination from feces or carcasses. Despite this, some similarities were found between feces and carcasses. In group analysis, phylogenetic similarities were detected in a 3/36 cluster (8.3%). Nevertheless, further studies are needed to improve consumer risk communication and access to clear and reliable information and health concerns on food labels.

In vitro evaluation of probiotic properties and antioxidant activities of Bifidobacterium strains from infant feces in the Uyghur population of northwestern China

Purpose

Bifidobacterium is an important probiotic used in food and medicine production. The probiotic properties of bifidobacteria are strain specific, so it is necessary to evaluate the probiotic properties of bifidobacteria isolated from specific populations, especially when developing products suitable for specific populations. The objective of this study was to evaluate the probiotic potential and safety of bifidobacteria isolated from healthy Uyghur infants from northwestern China.

Methods

In this study, antimicrobial activity, antibiotic sensitivity, hemolytic, acid and bile tolerance, hydrophobicity, co-aggregation, auto-aggregation, and antioxidant activity were evaluated.

Results

Based on antagonistic activity spectrum against seven intestinal pathogenic bacteria, 14 excellent strains were initially selected. Among 14 strains, four bifidobacteria strains (BF17-4, BF52-1, BF87-3, and BF88-5) were superior to strain Lactobacillus rhamnosus GG in cell surface hydrophobicity and auto-aggregation percentages and close to strain GG in co-aggregation with Escherichia coli EPEC O127: K63 (CICC 10411). The antioxidant activities of each of the 14 bifidobacteria strains varied with the cell components. Most of the strains were sensitive to all the antimicrobials tested, except kanamycin and amikacin.

Conclusion

BF17-4 and BF52-1 are good candidates for further in vivo studies and further used in functional foods.

Phylogenomic disentangling of the Bifidobacterium longum subsp. infantis taxon

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

Effect of in Ovo Inoculation of Bifidobacterium spp. on Growth Performance, Thyroid Activity, Ileum Histomorphometry, and Microbial Enumeration of Broilers

Early colonization by beneficial bacteria stimulates the function and development of the digestive tract, on which the performance and vitality of broilers rely. This experiment evaluated the effects of in ovo injection of bifidobacteria on the performance, thyroid activity, bacterial enumeration, and ileal histomorphometry of broiler chickens. A total of 360 fertile eggs were inoculated into the yolk sac, on day 17 of embryogenesis, and allocated to six experimental groups: negative control (not injected, G1), positive control (injected with sterilized distilled water, G2), and groups inoculated with 2 × 10⁸ CFU of Bifidobacterium bifidum, G3; B. animalis, G4; B. longum, G5; or B. infantis, G6. The results revealed an increase (P < 0.01) in body weight and weight gain in all treated groups increases of at least 5.38 and 8.27%, respectively, compared with the control. Feed consumption was not affected during all experimental periods, while the feed conversion ratio (FCR) was enhanced (P < 0.01) only for the overall experimental period (1-28 days of age). The G3 birds recorded the lowest FCR (1.38), while the highest was observed in G1 birds (1.57). Serum concentrations of thyroxin and triiodothyronine were elevated (P < 0.05) with probiotic inoculation. The antioxidant status and immune response of bifidobacteria injected birds were improved; the serum contents of superoxide dismutase and immunoglobulins Y, M, and A were increased (P < 0.05 and P < 0.01), while the malondialdehyde content was decreased (P < 0.01). Ileal architecture was improved in the bifidobacteria treated groups; the highest values of villus height and the villus height/crypt depth ratio were recorded in G3 (936.6 and 11.80) compared with those of G1 (537.1 and 6.93). Moreover, ileal lactic acid bacteria and Bifidobacterium spp. counts increased by at least 10.64 and 51.75%, while total coliform and bacterial counts reduced by at least 15.46 and 15.18%, respectively, compared with those of the control. In conclusion, all tested strains of bifidobacteria enhanced broiler growth performance, ileal function, and thyroid hormone metabolism without obvious differences among them.

Preventive Effects of Lactobacillus Mixture against Chronic Kidney Disease Progression through Enhancement of Beneficial Bacteria and Downregulation of Gut-Derived Uremic Toxins

Gut dysbiosis is a major contributor to adverse chronic kidney disease (CKD) progression, and microbiota-based strategies could be considered as a novel therapeutic and preventative target. In this study, a probiotic screening platform based on gut-derived uremic toxin-reducing probiotics was developed and the underlying mechanism was further verified through a 0.2% adenine-induced CKD mouse model. Two strains (Lactobacillus paracasei and Lactobacillus plantarum) were selected due to their high clearance ability and named Lactobacillus mix (Lm). The results showed that Lm significantly improved the kidney function by reducing kidney injury and fibrotic-related proteins. Furthermore, Lm decreased oxidative stress and proinflammatory reactions and elevated immune responses in the kidney. Importantly, Lm reversed gut dysbiosis and restored the abundance of commensal bacteria, especially short-chain fatty acid producers, leading to improved intestinal barrier integrity via modulation of microbial composition and metabolite production. Taken together, these findings provided evidence that Lm could be a preventive approach against CKD.

Efficacy of BOX-PCR fingerprinting for taxonomic discrimination of bifidobacterial species isolated from diverse sources

The genus Bifidobacterium are extensively used as probiotics in food applications, for their potential role to combat different lifestyle diseases. This has necessitated a great importance for their species, sub-species and even at the strain level characterization. In the present study, attempts have been made to target repetitive DNA element-based BOX-PCR fingerprinting to judge its potential in taxonomic discrimination of Bifidobacterium species. The BOXA1R primer-based repetitive PCR amplified products were analysed for 93 identified bifidobacterial isolates collected from diverse sources of human and animal origin along with 12 DSMZ procured standard reference strains. Dendrograms constructed from the fingerprint patterns of BOX-PCR differentiated all the isolated strains into 10 different groups, grouped with one standard reference isolates and successfully discriminated all isolates up to subspecies level as identified. The BOX-PCR method used in this study effectively resolved the taxonomic status and differentiated all 93 bifidobacterial species isolated from diverse faecal origins of human and animal samples.

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.

Dongshaea marina gen. nov., sp. nov., a facultatively anaerobic marine bacterium that ferments glucose with gas production

Two isolates of heterotrophic, facultatively anaerobic, marine bacteria, designated DM1 and DM2^T, were recovered from a lagoon sediment sample of Dongsha Island, Taiwan. Cells were Gram-reaction-negative rods. Nearly all of the cells were non-motile and non-flagellated during the late exponential to early stationary phase of growth, while a few of the cells exhibited motility with monotrichous flagellation. The two isolates required NaCl for growth and grew optimally at about 30 °C, 2-3 % NaCl and pH 7-8. They grew aerobically and could achieve anaerobic growth by fermenting d-glucose or other carbohydrates with production of acids and the gases, including CO₂ and H₂. Ubiquinone Q-8 was the only respiratory quinone. Cellular fatty acids were predominated by C_16 : 0, C_18 : 1ω7c and C_16 : 1ω7c. The major polar lipid was phosphatidylethanolamine. Strains DM1 and DM2^T had DNA G+C contents of 52.0 and 51.8 mol%, respectively, as determined by HPLC analysis. Phylogenetic analyses based on 16S rRNA gene sequences clearly indicated that the two isolates formed a distinct genus-level lineage in the family Aeromonadaceae of the class Gammaproteobacteria and was an outgroup with respect to a stable supragenic clade comprising species of the genera Oceanimonas, Oceanisphaera and Zobellella. The phylogenetic data and those from chemotaxonomic, physiological and morphological characterizations support the establishment of a novel species and genus inside the family Aeromonadaceae, for which the name Dongshaea marina gen. nov., sp. nov. is proposed. The type strain is DM2^T (=BCRC 81069^T=JCM 32096^T).

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.

Comparison of various molecular methods for rapid differentiation of intestinal bifidobacteria at the species, subspecies and strain level

BACKGROUND

Members of the genus Bifidobacterium are anaerobic Gram-positive Actinobacteria, which are natural inhabitants of human and animal gastrointestinal tract. Certain bifidobacteria are frequently used as food additives and probiotic pharmaceuticals, because of their various health-promoting properties. Due to the enormous demand on probiotic bacteria, manufacture of high-quality products containing living microorganisms requires rapid and accurate identification of specific bacteria. Additionally, isolation of new industrial bacteria from various environments may lead to multiple isolations of the same strain, therefore, it is important to apply rapid, low-cost and effective procedures differentiating bifidobacteria at the intra-species level. The identification of new isolates using microbiological and biochemical methods is difficult, but the accurate characterization of isolated strains may be achieved using a polyphasic approach that includes classical phenotypic methods and molecular procedures. However, some of these procedures are time-consuming and cumbersome, particularly when a large group of new isolates is typed, while some other approaches may have too low discriminatory power to distinguish closely related isolates obtained from similar sources.

RESULTS

This work presents the evaluation of the discriminatory power of four molecular methods (ARDRA, RAPD-PCR, rep-PCR and SDS-PAGE fingerprinting) that are extensively used for fast differentiation of bifidobacteria up to the strain level. Our experiments included 17 reference strains and showed that in comparison to ARDRA, genotypic fingerprinting procedures (RAPD and rep-PCR) seemed to be less reproducible, however, they allowed to differentiate the tested microorganisms even at the intra-species level. In general, RAPD and rep-PCR have similar discriminatory power, though, in some instances more than one oligonucleotide needs to be used in random amplified polymorphic DNA analysis. Moreover, the results also demonstrated a high discriminatory power of SDS-PAGE fingerprinting of whole-cell proteins. On the other hand, the protein profiles obtained were rather complex, and therefore, difficult to analyze.

CONCLUSIONS

Among the tested procedures, rep-PCR proved to be the most effective and reliable method allowing rapid differentiation of Bifidobacterium strains. Additionally, the use of the BOXA1R primer in the differentiation of 21 Bifidobacterium strains, newly isolated from infant feces, demonstrated slightly better discriminatory power in comparison to PCR reactions with the (GTG)5 oligonucleotide. Thus, BOX-PCR turned out to be the most appropriate and convenient molecular technique in differentiating Bifidobacterium strains at all taxonomic levels.

Bifidobacterium eulemuris sp. nov., isolated from faeces of black lemurs (Eulemur macaco)

Forty-three strains of bifidobacteria were isolated from the faeces of two adult black lemurs, Eulemur macaco. Thirty-four were identified as Bifidobacterium lemurum, recently described in Lemur catta. The nine remaining isolates were Gram-positive-staining, non-spore-forming, fructose-6-phosphate phosphoketolase-positive, microaerophilic, irregular rod-shaped bacteria that often presented Y- or V-shaped cells. Typing techniques revealed that these isolates were nearly identical, and strain LMM_E3^T was chosen as a representative and characterized further. Phylogenetic analysis based on 16S rRNA gene sequences clustered this isolate inside the genus Bifidobacterium and showed the highest levels of sequence similarity with B. lemurum DSM 28807^T (99.3 %), with Bifidobacterium pullorum LMG 21816^T and Bifidobacterium longum subsp. infantis ATCC 15697^T (96.4 and 96.3 %, respectively) as the next most similar strains. The hsp60 gene sequence of strain LMM_E3^T showed the highest similarity to that of Bifidobacterium stellenboschense DSM 23968^T (93.3 %), and 91.0 % similarity to that of the type strain of B. lemurum. DNA-DNA reassociation with the closest neighbour B. lemurum DSM 28807^T was found to be 65.4 %. The DNA G+C content was 62.3 mol%. Strain LMM_E3^T showed a peptidoglycan structure that has not been detected in bifidobacteria so far: A3α l-Lys-l-Ser-l-Thr-l-Ala. Based on the phylogenetic, genotypic and phenotypic data, strain LMM_E3^T represents a novel species within the genus Bifidobacterium, for which the name Bifidobacterium eulemuris sp. nov. is proposed; the type strain is LMM_E3^T ( = DSM 100216^T = JCM 30801^T).

Subspeciation of Bifidobacterium longum by multilocus approaches and amplified fragment length polymorphism: Description of B. longum subsp. suillum subsp. nov., isolated from the faeces of piglets

The species Bifidobacterium longum is currently divided into three subspecies, B. longum subsp. longum, B. longum subsp. infantis and B. longum subsp. suis. This classification was based on an assessment of accumulated information on the species' phenotypic and genotypic features. The three subspecies of B. longum were investigated using genotypic identification [amplified-fragment length polymorphism (AFLP), multilocus sequence analysis (MLSA) and multilocus sequence typing (MLST)]. By using the AFLP and the MLSA methods, we allocated 25 strains of B. longum into three major clusters corresponding to the three subspecies; the cluster comprising the strains of B. longum subsp. suis was further divided into two subclusters differentiable by the ability to produce urease. By using the MLST method, the 25 strains of B. longum were divided into eight groups: four major groups corresponding to the results obtained by AFLP and MLSA, plus four minor disparate groups. The results of AFLP, MLSA and MLST analyses were consistent and revealed a novel subspeciation of B. longum, which comprised three known subspecies and a novel subspecies of urease-negative B. longum, for which the name B. longum subsp. suillum subsp. nov. is proposed, with type strain Su 851(T)=DSM 28597(T)=JCM 19995(T).

Bifidobacterium lemurum sp. nov., from faeces of the ring-tailed lemur (Lemur catta)

Four Gram-positive-staining, microaerophilic, non-spore-forming, fructose-6-phosphate phosphoketolase-positive bacterial strains were isolated from a faecal sample of a 5-year-old ring-tailed lemur (Lemur catta). The strains showed a peculiar morphology, resembling a small coiled snake, a ring shape, or forming a little 'Y' shape. The isolated strains appeared identical, and LMC 13T was chosen as a representative strain and characterized further. Strain LMC 13T showed an A3β peptidoglycan type, similar to that found in Bifidobacterium longum. The DNA base composition was 57.2 mol% G+C. Almost-complete 16S rRNA, hsp60, rpoB, dnaJ, dnaG, purF, clpC and rpoC gene sequences were obtained, and phylogenetic relationships were determined. Comparative analysis of 16S rRNA gene sequences showed that strain LMC 13T showed the highest similarity to B. longum subsp. suis ATCC 27533T (96.65 %) and Bifidobacterium saguini DSM 23967T (96.64 %). Strain LMC 13T was located in an actinobacterial cluster and was more closely related to the genus Bifidobacteriumthan to other genera in the Bifidobacteriaceae. On the basis of these results, strain LMC 13T represents a novel species within the genus Bifidobacterium, for which the name Bifidobacterium lemurum sp. nov. is proposed; the type strain is LMC 13T ( = DSM 28807T = JCM 30168T).

Prebiotic Oligosaccharides: Comparative Evaluation Using In Vitro Cultures of Infants' Fecal Microbiomes

The objective of this study was to systematically assess the bifidogenic effect of three commonly used prebiotic products using in vitro cultures of infant fecal samples. Fresh stool samples collected from six term infants, each exclusively fed human milk (n = 3) or infant formula (n = 3), at 28 days of age were used as inocula. The following prebiotic products were added at concentrations applicable to infant formula: Vivinal GOS 15 (containing 28.5% galacto-oligosaccharide [GOS]) at 7.2 g/liter, Beneo HP (99.5% long-chain inulin [IN]) at 0.8 g/liter, Beneo Synergy 1 (enriched oligofructose and inulin [OF-IN]) at 4 g/liter, and a combination of Vivinal GOS 15 (7.2 g/liter) and Beneo HP (0.8 g/liter) (GOS-IN). The growth of total bacteria, Bifidobacterium, Bacteroides, Bifidobacterium longum, and Escherichia coli was quantified using specific quantitative PCR (qPCR). Bifidobacterium was also enumerated on selective Beerens agar plates, with representative colonies identified by sequencing of their 16S rRNA genes. Volatile fatty acids (VFA) and pH in the cultures were also determined. Irrespective of the feeding methods, the GOS product, either alone or in combination with Beneo HP, resulted in substantially higher growth of total bifidobacteria, and much of this growth was attributed to growth of B. longum. Beneo Synergy 1 also increased the abundance of total bifidobacteria and B. longum. Corresponding to the increases in these two bacterial groups, acetic acid concentrations were higher, while there was a trend of lower E. coli levels and pH. The lower pH and higher acetic acid concentration might be directly responsible for the lower E. coli population. At the concentrations studied, the GOS product was more bifidogenic and potent in inhibiting E. coli than the other products tested. These results suggest that supplementation of infant formula with GOS may increase intestinal bifidobacteria and benefit infant health.

Gut microbial diversity in rat model induced by rhubarb

Rhubarb is often used to establish chronic diarrhea and spleen (Pi)-deficiency syndrome animal models in China. In this study, we utilized the enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) method to detect changes in bacterial diversity in feces and the bowel mucosa associated with this model. Total microbial genomic DNA from the small bowel (duodenum, jejunum, and ileum), large bowel (proximal colon, distal colon, and rectum), cecum, and feces of normal and rhubarb-exposed rats were used as templates for the ERIC-PCR analysis. We found that the fecal microbial composition did not correspond to the bowel bacteria mix. More bacterial diversity was observed in the ileum of rhubarb-exposed rats (P<0.05). Furthermore, a 380 bp product was found to be increased in rhubarb-exposed rats both in faces and the bowel mucosa. The product was cloned and sequenced and showed high similarity with regions of the Bacteroides genome. AS a result of discriminant analysis with the SPSS software, the Canonical Discriminant Function Formulae for model rats was established.

Bifidobacterium aesculapii sp. nov., from the faeces of the baby common marmoset (Callithrix jacchus)

Six Gram-positive-staining, microaerophilic, non-spore-forming, fructose-6-phosphate phosphoketolase-positive bacterial strains with a peculiar morphology were isolated from faecal samples of baby common marmosets (Callithrix jacchus). Cells of these strains showed a morphology not reported previously for a bifidobacterial species, which resembled a coiled snake, always coiled or ring shaped or forming a 'Y' shape. Strains MRM 3/1(T) and MRM 4/2 were chosen as representative strains and characterized further. The bacteria utilized a wide range of carbohydrates and produced urease. Glucose was fermented to acetate and lactate. Strain MRM 3/1(T) showed a peptidoglycan type unique among members of the genus Bifidobacterium. The DNA base composition was 64.7 mol% G+C. Almost-complete 16S rRNA, hsp60, clpC and rpoB gene sequences were obtained and phylogenetic relationships were determined. Comparative analysis of 16S rRNA gene sequences showed that strains MRM 3/1(T) and MRM 4/2 had the highest similarities to Bifidobacterium scardovii DSM 13734(T) (94.6%) and Bifidobacterium stellenboschense DSM 23968(T) (94.5%). Analysis of hsp60 showed that both strains were closely related to B. stellenboschense DSM 23968(T) (97.5% similarity); however, despite this high degree of similarity, our isolates could be distinguished from B. stellenboschense DSM 23968(T) by low levels of DNA-DNA relatedness (30.4% with MRM 3/1(T)). Strains MRM 3/1(T) and MRM 4/2 were located in an actinobacterial cluster and were more closely related to the genus Bifidobacterium than to other genera in the family Bifidobacteriaceae. On the basis of these results, strains MRM 3/1(T) and MRM 4/2 represent a novel species within the genus Bifidobacterium, for which the name Bifidobacterium aesculapii sp. nov. is proposed; the type strain is MRM 3/1(T) ( = DSM 26737(T) = JCM 18761(T)).

Microbial characterization of probiotics--advisory report of the Working Group "8651 Probiotics" of the Belgian Superior Health Council (SHC)

When ingested in sufficient numbers, probiotics are expected to confer one or more proven health benefits on the consumer. Theoretically, the effectiveness of a probiotic food product is the sum of its microbial quality and its functional potential. Whereas the latter may vary much with the body (target) site, delivery mode, human target population, and health benefit envisaged microbial assessment of the probiotic product quality is more straightforward. The range of stakeholders that need to be informed on probiotic quality assessments is extremely broad, including academics, food and biotherapeutic industries, healthcare professionals, competent authorities, consumers, and professional press. In view of the rapidly expanding knowledge on this subject, the Belgian Superior Health Council installed Working Group "8651 Probiotics" to review the state of knowledge regarding the methodologies that make it possible to characterize strains and products with purported probiotic activity. This advisory report covers three main steps in the microbial quality assessment process, i.e. (i) correct species identification and strain-specific typing of bacterial and yeast strains used in probiotic applications, (ii) safety assessment of probiotic strains used for human consumption, and (iii) quality of the final probiotic product in terms of its microbial composition, concentration, stability, authenticity, and labeling.

Identification of species belonging to the Bifidobacterium genus by PCR-RFLP analysis of a hsp60 gene fragment

Background

Bifidobacterium represents one of the largest genus within the Actinobacteria, and includes at present 32 species. These species share a high sequence homology of 16S rDNA and several molecular techniques already applied to discriminate among them give ambiguous results.

The slightly higher variability of the hsp60 gene sequences with respect to the 16S rRNA sequences offers better opportunities to design or develop molecular assays, allowing identification and differentiation of closely related species. hsp60 can be considered an excellent additional marker for inferring the taxonomy of the members of Bifidobacterium genus.

Results

This work illustrates a simple and cheap molecular tool for the identification of Bifidobacterium species. The hsp60 universal primers were used in a simple PCR procedure for the direct amplification of 590 bp of the hsp60 sequence. The in silico restriction analysis of bifidobacterial hsp60 partial sequences allowed the identification of a single endonuclease (HaeIII) able to provide different PCR-restriction fragment length polymorphism (RFLP) patterns in the Bifidobacterium spp. type strains evaluated. The electrophoretic analyses allowed to confirm the different RFLP patterns.

Conclusions

The developed PCR-RFLP technique resulted in efficient discrimination of the tested species and subspecies and allowed the construction of a dichotomous key in order to differentiate the most widely distributed Bifidobacterium species as well as the subspecies belonging to B. pseudolongum and B. animalis.

Development of an ERIC sequence typing scheme for Laribacter hongkongensis, an emerging pathogen associated with community-acquired gastroenteritis and travellers’ diarrhoea

Laribacter hongkongensis is a potential emerging pathogen, associated with community-acquired diarrhoea. For epidemiological purposes, different molecular typing methods, such as pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing, have been developed for this pathogen. However, these methods require specialized equipment and costly reagents. More importantly, they are labour-intensive and time-consuming, which is not really suitable for foodborne disease outbreak investigations. In this study, we developed a rapid and reliable method using 22-mer primers specific for the enterobacterial repetitive intergenic consensus sequence (ERIC). PFGE was used for comparison, to evaluate this method. A total of 81 isolates of L. hongkongensis were examined: 79 isolates recovered from food of diverse origins and two strains derived from patients with L. hongkongensis-associated infection. Typing patterns and clustering analysis indicated that the 81 L. hongkongensis isolates were grouped into 21 and 13 genotypes by ERIC-PCR and PFGE, respectively. ERIC-PCR was found as reproducible as PFGE. A high percentage (70.4 %) of isolates yielded distinguishable ERIC-PCR patterns, which were concordant with the results from PFGE. These results suggest that ERIC-PCR is valuable for use in the epidemiological investigation of L. hongkongensis.

Evaluation of strain-specific primers for identification of Lactobacillus rhamnosus GG

Lactobacillus rhamnosus strain GG (ATCC 53103) is one of the most widely studied and commercialized probiotic strains, and thus strain-specific identification for the strain is highly valuable. In this study, two published PCR-based identification methods for strain GG, a transposase gene-targeting system and a phage-related gene-targeting system, were evaluated. The former produced amplicons from eight of the 41 strains tested and the phage-related system from five of the tested strains, including the strain GG. Fingerprinting analysis indicated that the strains LMG 18025, LMG 18030, and LMG 18038, which had an amplicon by the former system but none by the latter, were genetically distinguishable from L. rhamnosus GG at strain level. Strains LMG 23320, LMG 23325, LMG 23534, and LMG 25859 showed profiles very similar to that of the strain GG, suggesting that these strains might be identical to GG or derivative strains of it. The results here indicated that the phage-related gene-targeting system is a good tool for accurate identification of L. rhamnosus GG. This system would be able to detect both the original L. rhamnosus GG and its derivative strains.

Characterization of Bifidobacterium spp. strains for the treatment of enteric disorders in newborns

Several studies support the use of probiotics for the treatment of minor gastrointestinal problems in infants. Positive effects on newborn colics have been evidenced after administration of Lactobacillus strains, whereas no studies have been reported regarding the use of bifidobacteria for this purpose. This work was therefore aimed at the characterization of Bifidobacterium strains capable of inhibiting the growth of pathogens typical of the infant gastrointestinal tract and of coliforms isolated from colic newborns. Among the 46 Bifidobacterium strains considered, 16 showed high antimicrobial activity against potential pathogens; these strains were further characterized from a taxonomic point of view, for the presence and transferability of antibiotic resistances, for citotoxic effects and adhesion to nontumorigenic gut epithelium cell lines. Moreover, their ability to stimulate gut health by increasing the metabolic activity and the immune response of epithelial cells was also studied. The examination of all these features allowed to identify three Bifidobacterium breve strains and a Bifidobacterium longum subsp. longum strain as potential probiotics for the treatments of enteric disorders in newborns such as infantile colics. A validation clinical trial involving the selected strains is being planned.

Manufacturing process influences properties of probiotic bacteria

Production and manufacturing methods and the food carrier may influence the properties of probiotic strains, and have an impact on the outcome of clinical intervention studies. The aim of the present study was to establish whether the properties of a specific probiotic strain, Lactobacillus rhamnosus GG, may differ depending on the product and source of the strain. In total, fifteen different L. rhamnosus isolates, among them fourteen labelled as L. rhamnosus GG, were isolated from specific probiotic products. The micro-organisms were phenotypically and genotypically characterised. Their adhesion properties were compared using the human intestinal mucus model, and the ability of the isolates to influence model pathogen adhesion to human colonic mucus was assessed. All L. rhamnosus isolates used were confirmed as members of the species L. rhamnosus. Except the reference strain OL, all L. rhamnosus isolates showed randomly amplified polymorphic DNA, enterobacterial repetitive intergenic consensus and pulsed-field gel electrophoresis profiles identical to that of L. rhamnosus GG (ATCC 53103). All L. rhamnosus isolates showed similar tolerance to acid and were able to bind to human colonic mucus. However, pathogen exclusion by inhibition and competition varied significantly among the different L. rhamnosus isolates and pathogens tested. The results suggest that different sources of the same probiotic may have significantly altered strain properties. This should be considered in in vivo studies on human subjects and also for quality control of probiotic products.

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.

Differentiation of Bifidobacterium species using partial RNA polymerase {beta}-subunit (rpoB) gene sequences

Partial RNA polymerase β-subunit gene (rpoB) sequences (315 bp) were determined and used to differentiate the type strains of 23 species of the genus Bifidobacterium. The sequences were compared with those of the partial hsp60 (604 bp) and 16S rRNA genes (1475 or 1495 bp). The rpoB gene sequences showed nucleotide sequence similarities ranging from 84.1 % to 99.0 %, while the similarities of the hsp60 sequences ranged from 78.5 % to 99.7 % and the 16S rRNA gene sequence similarities ranged from 89.4 % to 99.2 %. The phylogenetic trees constructed from the sequences of these three genes showed similar clustering patterns, with the exception of several species. The Bifidobacterium catenulatum-Bifidobacterium pseudocatenulatum, Bifidobacterium pseudolongum subsp. pseudolongum-Bifidobacterium pseudolongum subsp. globosum and Bifidobacterium gallinarum-Bifidobacterium pullorum-Bifidobacterium saeculare groups were more clearly differentiated in the partial rpoB and hsp60 gene sequence trees than they were in the 16S rRNA gene tree. Based on sequence similarities and tree topologies, the newly determined rpoB gene sequences are suitable molecular markers for the differentiation of species of the genus Bifidobacterium and support various other molecular tools used to determine the relationships among species of this genus.

ERIC-PCR-based strain-specific detection of phenol-degrading bacteria in activated sludge of wastewater treatment systems

AIMS

To evaluate the use of Enterobacterial Repetitive Intergenic Consensus PCR (ERIC-PCR)-derived probes and primers to specifically detect bacterial strains in an activated sludge microbial community.

METHODS AND RESULTS

ERIC-PCR was performed on two phenol-degrading bacterial strains, Arthrobacter nicotianae P1-7 and Klebsiella sp. P8-14. Their amplicons were DIG labelled for use as probes and then hybridized with ERIC-PCR fingerprints. The results showed the distinct band patterns for both bacterial strains. Strain-specific PCR primers were designed based on the sequences of ERIC-PCR bands. The DNA of each of these strains was successfully detected from its mixture with activated sludge DNA, either by using their respective ERIC-PCR-based probes for hybridization or by using species-specific primers for amplification, with higher sensitivity by latter method.

CONCLUSIONS

Two phenol-degrading bacterial strains were identified from a mixture of activated sludge by using ERIC-PCR-based methods.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study demonstrated that the bacteria, which have important functions in complex wastewater treatment microbial communities, could be specifically detected by using ERIC-PCR fingerprint-based hybridization or amplification.

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.

Isolation and identification of bifidobacteriaceae from human saliva

Bifidobacteriaceae were isolated from saliva and infected dentine by using a mupirocin-based selective medium. Of the saliva samples, 94% harbored bifids. The mean concentration (+/- the standard error) was 4.46 (+/-0.12) log(10)(CFU per ml + 1), and the predominant isolates were Bifidobacterium dentium, B. longum, Scardovia inopinata, Parascardovia denticolens, and Alloscardovia omnicolens.

Orthogonal array design in optimizing ERIC-PCR system for fingerprinting rat's intestinal microflora

AIMS

The aim of the present study was to rapidly optimize enterobacterial repetitive intergenic consensus (ERIC)-PCR amplification systems for fingerprinting rat's intestinal microflora.

METHODS AND RESULTS

Orthogonal array design and statistic analysis methods were attempted to rapidly optimize ERIC-PCR reaction system for fingerprinting intestinal microflora. The results showed that variations of the four factors (Mg(2+), dNTP, primer and HotstarTaq polymerase concentrations) changed the fingerprinting patterns significantly. The order of effects of those factors on fingerprinting patterns was primers (F = 274.000, P = 0.000), Hotstar Taq polymerase (F = 197.000, P = 0.001), Mg(2+) (F = 181.000, P = 0.001) and dNTP (F = 27.000, P = 0.011). The optimal ERIC-PCR condition was containing 200 micromol l(-1) dNTP, 2.5 mmol l(-1) Mg(2+), 0.4 micromol l(-1) primer, 1 U HotstarTaq DNA polymerase namely 25 microl reaction system, which is proved to be a simple, fast and reliable method suitable for fingerprinting rat's intestinal microflora.

CONCLUSIONS

The results suggest that Mg(2+), dNTP, primer and HotstarTaq polymerase concentrations play important roles on ERIC-PCR fingerprinting patterns. Orthogonal array design is a considerable method to optimize ERIC-PCR reaction system for its rapidness, simplicity, potential to investigate mutual effects of parameters.

SIGNIFICANCE AND IMPACT OF THE STUDY

It is the first report on optimization of ERIC-PCR amplification systems for fingerprinting intestinal microflora using orthogonal array design or statistic analysis methods and systematically observing the effects of variables of reaction conditions.

Molecular characterization of Salmonella isolates by REP-PCR and RAPD analysis

Eighteen Salmonella isolates from both human and food (non-human) sources (fish, meat, and poultry) were characterized using conventional culture methods, biochemical, serological, and molecular analyses. REP-PCR and RAPD produced DNA profiles for differentiation purposes. Enterobacterial repetitive intergenic consensus (ERIC), repetitive extragenic palindronic (REP) and BOXAIR primers were selected for REP-PCR and two arbitrary primers, namely OPP-16 and OPS-11 were used for RAPD to generate DNA fingerprints from the Salmonella isolates. REP-PCR method showed greater discriminatory power in differentiating closely related strains of the related strains of Salmonella and produced more complex banding patterns as compared with RAPD. A dendogram was constructed with both sets of profiles using SPSS Version 13.0 computer software and showed that most human isolates were separately clustered from the non-human isolates. Two of the human isolates were closely related to some of the non-human isolates. A good correlation was also observed between the serogrouping of the O antigen and the molecular profiles obtained from REP-PCR and RAPD data of the Salmonella isolates. The results of a principal coordinate analysis (PCA) corresponded to the clustering in the dendrogram.

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.

Advanced molecular tools for the identification of lactic acid bacteria

Recent years have seen an explosion in the development and application of molecular tools for identifying microbes and analyzing their activity. These tools are increasingly applied to strains of lactic acid bacteria (LAB), including those used in fermentation and as well as those marketed as probiotics, for identification and analysis of their activity. Many of these tools are based on 16S ribosomal DNA sequences and exploit either hybridization or PCR techniques. Furthermore, complete or partial genomes of various LAB and bifidobacteria have been determined and offer omics-based approaches to analyze the activity of the bacteria provided that the mechanisms of their action are known. Finally, fluorescent probes coupled to flow cytometry are used to monitor the physiological capacity of bacterial cells in situ. All these approaches can be used for the screening and selection of LAB, assessing their role in fermentation and flavor development in fermented products. Additional aspects of probiotic LAB include their viability and vitality during processing and analysis of their presence, persistence, and performance in the gastrointestinal tract. An overview of these approaches is provided, and specific examples of their application to lactic cultures are presented. Because of their abundant use in tracing and tracking of LAB, a complete listing of 16S ribosomal RNA probes for lactobacilli and bifidobacteria is provided.

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.

Culture-dependent and culture-independent qualitative analysis of probiotic products claimed to contain bifidobacteria

A total of 58 probiotic products obtained worldwide, which were claimed to contain Bifidobacterium strains (including 22 yoghurts, 5 dairy fruit drinks, 28 food supplements and 3 pharmaceutical preparations) were investigated in parallel using a culture-dependent and a culture-independent approach. Three isolation media previously reported as selective for Bifidobacterium were evaluated for their suitability in the quality analysis of these products. Subsequently, possible bifidobacterial colonies were picked from the best medium and identified by means of rep-PCR fingerprinting using the BOX primer (BOX-PCR). Bifidobacterium animalis subsp. lactis, formerly classified as Bifidobacterium lactis, was most frequently found, but strains belonging to Bifidobacterium longum biotypes longum and infantis, Bifidobacterium bifidum and Bifidobacterium breve were recovered also. In parallel, all products were also subjected to culture-independent analysis which involved a nested-PCR step on total bacterial DNA extracted directly from the product, followed by separation of the amplicons by Denaturing Gradient Gel Electrophoresis (DGGE) and subsequent identification of species from the band patterns. By conventional cultivation, 70.7% of the products analysed were found to contain culturable bifidobacteria whereas by culture-independent DGGE analysis members of the genus Bifidobacterium could be detected in 96.5% of the analysed products. Genotypic characterization of a number of bifidobacterial isolates at the strain level by means of Pulsed-Field Gel Electrophoresis (PFGE) revealed a relatively high degree of genomic homogeneity among the Bifidobacterium strains currently used in the probiotic industry.

Evaluation of amplified ribosomal DNA restriction analysis (ARDRA) and species-specific PCR for identification of Bifidobacterium species

Molecular biological methods based on genus-specific PCR, species-specific PCR, and amplified ribosomal DNA restriction analysis (ARDRA) of two PCR amplicons (523 and 914bp) using six restriction enzymes were used to differentiate among species of Bifidobacterium. The techniques were established using DNA from 16 type and reference strains of bifidobacteria of 11 species. The discrimination power of 914bp amplicon digestion was higher than that of 523bp amplicon digestion. The 914bp amplicon digestion by six restrictases provided unique patterns for nine species; B. catenulatum and B. pseudocatenulatum were not differentiated yet. The NciI digestion of the 914bp PCR product enabled to discriminate between each of B. animalis, B. lactis, and B. gallicum. The reference strain B. adolescentis CCM 3761 was reclassified as a member of the B. catenulatum/B. pseudocatenulatum group. The above-mentioned methods were applied for the identification of seven strains of Bifidobacterium spp. collected in the Culture Collection of Dairy Microorganisms (CCDM). The strains collected in CCDM were differentiated to the species level. Six strains were identified as B. lactis, one strain as B. adolescentis.

Gene structure and transcriptional organization of the dnaK operon of Bifidobacterium breve UCC 2003 and application of the operon in bifidobacterial tracing

The incorporation and delivery of bifidobacterial strains as probiotic components in many food preparations expose these microorganisms to a multitude of environmental insults, including heat and osmotic stresses. We characterized the dnaK gene region of Bifidobacterium breve UCC 2003. Sequence analysis of the dnaK locus revealed four genes with the organization dnaK-grpE-dnaJ-ORF1, whose deduced protein products display significant similarity to corresponding chaperones found in other bacteria. Northern hybridization and real-time LightCycler PCR analysis revealed that the transcription of the dnaK operon was strongly induced by osmotic shock but was not induced significantly by heat stress. A 4.4-kb polycistronic mRNA, which represented the transcript of the complete dnaK gene region, was detected. Many other small transcripts, which were assumed to have resulted from intensive processing or degradation of this polycistronic mRNA, were identified. The transcription start site of the dnaK operon was determined by primer extension. Phylogenetic analysis of the available bifidobacterial grpE and dnaK genes suggested that the evolutionary development of these genes has been similar. The phylogeny derived from the various bifidobacterial grpE and dnaK sequences is consistent with that derived from 16S rRNA. The use of these genes in bifidobacterial species as an alternative or complement to the 16S rRNA gene marker provides sequence signatures that allow a high level of discrimination between closely related species of this genus.

Characterization of the groEL and groES loci in Bifidobacterium breve UCC 2003: genetic, transcriptional, and phylogenetic analyses

The bacterial heat shock response is characterized by the elevated expression of a number of chaperone complexes, including the GroEL and GroES proteins. The groES and groEL genes are highly conserved among eubacteria and are typically arranged as an operon. Genome analysis of Bifidobacterium breve UCC 2003 revealed that the groES and groEL genes are located in different chromosomal regions. The heat inducibility of the groEL and groES genes of B. breve UCC 2003 was verified by slot blot analysis. Northern blot analyses showed that the cspA gene is cotranscribed with the groEL gene, while the groES gene is transcribed as a monocistronic unit. The transcription initiation sites of these two mRNAs were determined by primer extension. Sequence and transcriptional analyses of the region flanking the groEL and groES genes of various bifidobacteria revealed similar groEL-cspA and groES gene units, suggesting a novel genetic organization of these chaperones. Phylogenetic analysis of the available bifidobacterial groES and groEL genes suggested that these genes evolved differently. Discrepancies in the phylogenetic positioning of groES-based trees make this gene an unreliable molecular marker. On the other hand, the bifidobacterial groEL gene sequences can be used as an alternative to current methods for tracing Bifidobacterium species, particularly because they allow a high level of discrimination between closely related species of this genus.

Bifidobacterium lactis DSM 10140: identification of the atp (atpBEFHAGDC) operon and analysis of its genetic structure, characteristics, and phylogeny

The atp operon is highly conserved among eubacteria, and it has been considered a molecular marker as an alternative to the 16S rRNA gene. PCR primers were designed from the consensus sequences of the atpD gene to amplify partial atpD sequences from 12 Bifidobacterium species and nine Lactobacillus species. All PCR products were sequenced and aligned with other atpD sequences retrieved from public databases. Genes encoding the subunits of the F(1)F(0)-ATPase of Bifidobacterium lactis DSM 10140 (atpBEFHAGDC) were cloned and sequenced. The deduced amino acid sequences of these subunits showed significant homology with the sequences of other organisms. We identified specific sequence signatures for the genus Bifidobacterium and for the closely related taxa Bifidobacterium lactis and Bifidobacterium animalis and Lactobacillus gasseri and Lactobacillus johnsonii, which could provide an alternative to current methods for identification of lactic acid bacterial species. Northern blot analysis showed that there was a transcript at approximately 7.3 kb, which corresponded to the size of the atp operon, and a transcript at 4.5 kb, which corresponded to the atpC, atpD, atpG, and atpA genes. The transcription initiation sites of these two mRNAs were mapped by primer extension, and the results revealed no consensus promoter sequences. Phylogenetic analysis of the atpD genes demonstrated that the Lactobacillus atpD gene clustered with the genera Listeria, Lactococcus, Streptococcus, and Enterococcus and that the higher G+C content and highly biased codon usage with respect to the genome average support the hypothesis that there was probably horizontal gene transfer. The acid inducibility of the atp operon of B. lactis DSM 10140 was verified by slot blot hybridization by using RNA isolated from acid-treated cultures of B. lactis DSM 10140. The rapid increase in the level of atp operon transcripts upon exposure to low pH suggested that the ATPase complex of B. lactis DSM 10140 was regulated at the level of transcription and not at the enzyme assembly step.

Comparative sequence analysis of the tuf and recA genes and restriction fragment length polymorphism of the internal transcribed spacer region sequences supply additional tools for discriminating Bifidobacterium lactis from Bifidobacterium animalis

The relationship between Bifidobacterium lactis and Bifidobacterium animalis was examined by comparative analysis of tuf and recA gene sequences and by restriction fragment length polymorphism analysis of their internal 16S-23S transcribed spacer region sequences. The bifidobacterial strains investigated could be divided into two distinct groups within a single species based on the tuf, recA, and 16S-23S spacer region sequence analysis. Therefore, all strains of B. lactis and B. animalis could be unified as the species B. animalis and divided into two subspecies, Bifidobacterium animalis subsp. lactis and Bifidobacterium animalis subsp. animalis.

Identification and characterization of simple sequence repeats in the genomes of Shigella species

A variety of simple sequence repeats (SSRs) have been identified in the genome of Shigella flexneri serotype 2a (strain Sf301), an enteric pathogen that causes bacillary dysentery in man. The distribution of SSRs, with unit length ranging from 1 to 9 nucleotides, was biased in different regions of the genome. The tri-, tetra- and hexanucleotide SSRs prevailed in the coding regions while the mono- and dinucleotide SSRs were more common in the noncoding regions. Many intergenic SSRs are less than 30 bp away from the downstream open reading frames (ORFs), suggesting a potential role in transcriptional regulation. To study polymorphism of SSRs, we compared 17 coding-region SSRs from strain Sf301 with the corresponding sequences from 23 other strains of four Shigella species. Five chromosomal loci were found to be polymorphic, of which those from S. flexneri strains were most variable. Particularly interesting is the C5-1 locus in the coding sequence of the hcaD gene encoding a subunit of ferredoxin reductase. Depending on the insertion of variable numbers of the unit sequence (CGCAG), the Shigella hcaD genes can encode truncated products due to premature stop codons or frame shifts, or products with extended core alpha helices that leads to radical alterations in the predicted tertiary structure. Hence, SSRs may serve as genotyping markers for epidemiological investigations, and may offer insights into evolutionary adaptation of the pathogens.