Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth

Background

Bifidobacteria are frequently proposed to be associated with good intestinal health primarily because of their overriding dominance in the feces of breast fed infants. However, clinical feeding studies with exogenous bifidobacteria show they don't remain in the intestine, suggesting they may lose competitive fitness when grown outside the gut.

Results

To further the understanding of genetic attenuation that may be occurring in bifidobacteria cultures, we obtained the complete genome sequence of an intestinal isolate, Bifidobacterium longum DJO10A that was minimally cultured in the laboratory, and compared it to that of a culture collection strain, B. longum NCC2705. This comparison revealed colinear genomes that exhibited high sequence identity, except for the presence of 17 unique DNA regions in strain DJO10A and six in strain NCC2705. While the majority of these unique regions encoded proteins of diverse function, eight from the DJO10A genome and one from NCC2705, encoded gene clusters predicted to be involved in diverse traits pertinent to the human intestinal environment, specifically oligosaccharide and polyol utilization, arsenic resistance and lantibiotic production. Seven of these unique regions were suggested by a base deviation index analysis to have been precisely deleted from strain NCC2705 and this is substantiated by a DNA remnant from within one of the regions still remaining in the genome of NCC2705 at the same locus. This targeted loss of genomic regions was experimentally validated when growth of the intestinal B. longum in the laboratory for 1,000 generations resulted in two large deletions, one in a lantibiotic encoding region, analogous to a predicted deletion event for NCC2705. A simulated fecal growth study showed a significant reduced competitive ability of this deletion strain against Clostridium difficile and E. coli. The deleted region was between two IS30 elements which were experimentally demonstrated to be hyperactive within the genome. The other deleted region bordered a novel class of mobile elements, termed mobile integrase cassettes (MIC) substantiating the likely role of these elements in genome deletion events.

Conclusion

Deletion of genomic regions, often facilitated by mobile elements, allows bifidobacteria to adapt to fermentation environments in a very rapid manner (2 genome deletions per 1,000 generations) and the concomitant loss of possible competitive abilities in the gut.

Comparative genomics of the lactic acid bacteria

Lactic acid-producing bacteria are associated with various plant and animal niches and play a key role in the production of fermented foods and beverages. We report nine genome sequences representing the phylogenetic and functional diversity of these bacteria. The small genomes of lactic acid bacteria encode a broad repertoire of transporters for efficient carbon and nitrogen acquisition from the nutritionally rich environments they inhabit and reflect a limited range of biosynthetic capabilities that indicate both prototrophic and auxotrophic strains. Phylogenetic analyses, comparison of gene content across the group, and reconstruction of ancestral gene sets indicate a combination of extensive gene loss and key gene acquisitions via horizontal gene transfer during the coevolution of lactic acid bacteria with their habitats.

Sulfur metabolism in bacteria associated with cheese

Metabolism of sulfur in bacteria associated with cheese has long been a topic of interest. Volatile sulfur compounds, specifically methanethiol, are correlated to desirable flavor in Cheddar cheese, but their definitive role remains elusive. Only recently have enzymes been found that produce this compound in bacteria associated with cheese making. Cystathionine beta- and gamma-lyase are found in lactic acid bacteria and are capable of producing methanethiol from methionine. Their primary function is in the metabolism of cysteine. Methionine gamma-lyase produces methanethiol from methionine at a higher efficiency than the cystathionine enzymes. This enzyme is found in brevibacteria, bacilli, and pseudomonads. Addition of brevibacteria containing this enzyme improves Cheddar cheese flavor. Despite recent progress in sulfur metabolism more information is needed before cheese flavor associated with sulfur can be predicted or controlled.

[Severe interstitial lung disease from pathologic gastroesophageal reflux in children]

Interstitial lung diseases comprise a heterogeneous group of pulmonary conditions that cause restrictive lung disease of poor prognosis, especially if growth failure, pulmonary hypertension and fibrosis appears. We report on the case of a girl of 11 years of age who suffered from severe nonallergic asthma in early childhood and who developed severe interstitial pulmonary disease caused by gastro-oesophageal reflux at the age of 8 years. This diagnosis was established by lung biopsy, bronchoalveolar lavage and a high amount of lipid-laden alveolar macrophages, 2-level pH measurement and oesophageal biopsy. Because therapy with oral and inhaled steroids failed and Omeprazol showed benificial effects, hemifundoplication according to THAL was performed. At present the lung function is clearly normal and there is no need of any medicaments. Following the history, we can assume the pathological gastro-oesophageal reflux to be the cause of the disease. It is important to state that there were no typical symptoms at any time pointing to gastro-oesophageal reflux disease. The development of pulmonary disease by pathological reflux is very often caused by "silent aspiration". Very typically there are no symptoms such as vomiting, heartburn and pain but only signs of chronic lung disease.

[Reference values of hemosiderin-laden alveolar macrophages in bronchoalveolar lavage in children]

Pulmonary haemosiderosis is a rare disease of unknown etiology, mainly affecting children and adolescents. Pulmonary haemosiderosis may occur in association with several respiratory or other disease (Lupus erythematosus, Goodpastures syndrome). Delay in diagnosing can lead to fatal complications. BAL appears to be the method of choice to detect haemosiderin-laden macrophages. No reference values are available for children to date. 64 bronchoalveolar lavages were performed to establish reference values of haemosiderin-laden macrophages in children. Less haemosiderin was found in children compared to adults, and hence a new haemosiderin score was established for paediatric patients. Compared to healthy children, no elevated haemosiderine levels were found in children with chronic pulmonary disease such as bronchiectasis or chronic aspiration caused by gastro-oesophageal reflux. Therefore even a mildly increased amount of haemosiderin-laden macrophages in children requires medical attention.

Isolation and characterization of acid- and bile-tolerant isolates from strains of Lactobacillus acidophilus

Lactic acid bacteria have been reported to be useful as a health adjunct and are commonly added to food as the delivery mechanism. The literature contains many conflicting observations for their proposed benefits, and the mechanism of action is undefined. One source of variation is the large number of strains used without proper controls supplemented. Additionally, many of the organisms are not characterized for their acid shock response or the acid-tolerance response, which are known to vary among bacterial species. Our objective was to isolate acid-resistant and bile-resistant variants of Lactobacillus acidophilus and to determine the phenotypic changes. The acid- and bile-tolerant isolates were obtained using natural selection techniques after sequential exposure to hydrochloric acid (pH 3.5 to 7.0) and mixed bile salts. The acid- and bile-tolerant isolates retained their ability to grow at pH 3.5 with 0.3% bile after the selective pressure was removed and reapplied. Isolates varied from their parents for stability in freezing, lactose utilization, protease activity, aminopeptidase activity, plasmid profile, and cell-wall fatty acid profile. These data suggest that the isolated acid- and bile-tolerant isolates possess growth advantages over that of the parents under stress conditions and may be considered as candidates for probiotic strains after further characterization with animal models.

[Pulmonary hemosiderosis and gastroesophageal reflux in an infant]

Pulmonary hemosiderosis (PH) has been described in association with a variety of immunological and non-immunological diseases. It is characterised by iron-deficiency anaemia, hemoptysis and diffuse pulmonary infiltrates based on recurrent intraalveolar hemorrhages. We present the case of a child with pulmonary hemosiderosis and a pathological gastroesophageal reflux activity. The child suffered from recurrent anaemic episodes the age of three months (hemoglobin level up to 5.4 g/dl). The symptoms decreased after removal of the gastroesophageal reflux and accompanying steroid therapy. There has been one relapse of pulmonary hemorrhage seven months later (hemoglobin level 6.1 g/dl). Since then the patient has been in good general condition and the steroid was slowly reduced. No more anaemic episodes occurred. We discuss a possible association of pathological gastroesophageal reflux activity in pulmonary hemosiderosis.

Structure and chromosomal localization of the human gene for a brain form of prostaglandin D2 synthase

We have cloned and characterized the human gene for the 21-kDa brain form of prostaglandin D2 synthase. The gene was isolated from a human genomic lambda library and spans 3600 base pairs. It consists of seven exons and six introns. Southern blot analysis indicates that there is a single copy of the gene in the haploid genome. The transcriptional start site was mapped to a G residue 74 base pairs 5' of the ATG initiation codon. A TATA box-like element (ATAAATA) is situated 21 base pairs upstream of the mRNA start site. The gene was mapped to chromosome 9 bands q34.2-q34.3. The gene bears close resemblance to the genes for murine major urinary protein and ovine beta-lactoglobulin.

[Immunoscintigraphy using 111In-DTPA-labeled monoclonal antibodies: comparison with ECT and planar scintigraphy]

The present study was done in order to examine if the use of 111In-DTPA-labeled MAb fragments in place of 131I-labeled MAb fragments increases the sensitivity of tomographic immunoscintigraphy to reach the level of that of planar imaging techniques. In 11 patients with various primary tumors, local recurrences or metastases [colorectal carcinoma (n = 7), ovarian carcinoma (n = 2), papillary thyroid carcinoma (n = 1), undifferentiated carcinoma of the lung (n = 1)], immunoscintigraphy (IS) was carried out using 111In-DTPA-labeled F(ab')2 fragments of various MAbs (anti-CEA, OC 125, anti-hTG) and planar and tomographic imaging were compared intra-individually. By conventional diagnostic procedures, the presence of a tumor mass was confirmed (transmission computer tomography, ultrasound) or verified (131I whole-body scintigraphy, histology) in all cases. Immunoscintigraphy was positive in 9 out of 11 cases by ECT and in 10 out of 11 cases by planar imaging. When using 111In-labeled MAb fragments, intra-individual comparison of ECT and planar imaging resulted in a similar sensitivity. The increased sensitivity of ECT using this tracer in contrast to 131I-labeled MAb fragments may be attributed to the fact that the physical properties of 111In are much more suitable for the gamma cameras most commonly used (single detector, 3/8'' crystal); using 111In-labeled MAb fragments, count rates sufficient for ECT can be obtained within a reasonable acquisition time. This allows to combine IS with the advantages of ECT regarding tumour localization and prevention of artefacts due to superposition of background.

Immunszintigraphie mit 111ln-DTPA-markierten monoklonalen Antikörpern: Vergleich zwischen ECT und planarer Szintigraphie

The present study was done in order to examine if the use of111ln-DTPA- labeled MAb fragments in place of 131l-labeled MAb fragments increases the sensitivity of tomographic immunoscintigraphy to reach the level of that of planar imaging techniques. In 11 patients with various primary tumors, local recurrences or metastases [colorectal carcinoma (n = 7), ovarian carcinoma (n = 2), papillary thyroid carcinoma (n = 1), undifferentiated carcinoma of the lung (n = 1)], immunoscintigraphy (IS) was carried out using 111ln-DTPA- labeled F(ab’)2 fragments of various MAbs (anti-CEA, OC 125, anti-hTG) and planar and tomographic imaging were compared intraindividually. By conventional diagnostic procedures, the presence of a tumor mass was confirmed (transmission computer tomography, ultrasound) or verified (131l whole-body scintigraphy, histology) in all cases. Immunoscintigraphy was positive in 9 out of 11 cases by ECT and in 10 out of 11 cases by planar imaging. When using 111 In-labeled MAb fragments, intraindividual comparison of ECT and planar imaging resulted in a similar sensitivity. The increased sensitivity of ECT using this tracer in contrast to 131l-labeled MAb fragments may be attributed to the fact that the physical properties of111 In are much more suitable for the gamma cameras most commonly used (single detector, 3/8” crystal); using 111 In-labeled MAb fragments, count rates sufficient for ECT can be obtained within a reasonable acquisition time. This allows to combine IS with the advantages of ECT regarding tumour localization and prevention of artefacts due to superposition of background.

Symbolic coordinate anatomy for neurology (SCAN)

Our laboratory is responsible for development and maintenance of CADUCEUS (Formerly INTERNIST-1), a computer program to provide expert advice to the clinician in the realm of medical diagnosis. In order to extend its success in internal medicine into neurology, it was necessary to provide a paradigm for neuroanatomic reasoning. In our anatomic knowledge base (SCAN), the nervous system is partitioned into a hierarchical set of nested cubes. In the computer memory, a symbol for each cube has attached to it lists of structures that are wholly or partially within the cube. The structures may be simple (e.g., right locus ceruleus) or complex (e.g., midbrain). Lists of cubes belonging to particular vascular territories as well as systems (e.g., visual) are also maintained. Thus, computation of anatomic localization from a given symptom or finding is facilitated as well as characterization of consequences of vascular lesions or neighborhood effects from mass lesions.