Diversity and abundance of single-stranded DNA viruses in human feces

In this study, we investigated the abundance and diversity of single-stranded DNA (ssDNA) viruses in fecal samples from five healthy individuals through a combination of serial filtration and CsCl gradient ultracentrifugation. Virus abundance ranged from 10⁸ to 10⁹ per gram of feces, and virus-to-bacterium ratios were much lower (less than 0.1) than those observed in aquatic environments (5 to 10). Viral DNA was extracted and randomly amplified using phi29 polymerase and analyzed through high-throughput 454 pyrosequencing. Among 400,133 sequences, an average of 86.2% viromes were previously uncharacterized in public databases. Among previously known viruses, double-stranded DNA podophages (52 to 74%), siphophages (11 to 30%), myophages (1 to 4%), and ssDNA microphages (3 to 9%) were major constituents of human fecal viromes. A phylogenetic analysis of 24 large contigs of microphages based on conserved capsid protein sequences revealed five distinct newly discovered evolutionary microphage groups that were distantly related to previously known microphages. Moreover, putative capsid protein sequences of five contigs were closely related to prophage-like sequences in the genomes of three Bacteroides and three Prevotella strains, suggesting that Bacteroides and Prevotella are the sources of infecting microphages in their hosts.     

Development of bacterial and bifidobacterial communities in feces of newborn babies

Microbial 16S rDNA from babies' fecal samples were amplified by PCR, and analysed by denaturing gradient gel electrophoresis (DGGE), cloning and sequencing. PCR-DGGE profiles were used to follow in time the colonization of the intestine by bacteria. Four healthy babies, one baby who received antibiotics and their parents participated to the present study to determine the extent to which administration of antibiotics can modify the bacterial colonization of neonatal human gut and verify the influence of parental factors on the formation of the fecal bacterial community. In the healthy babies, Escherichia coli or bacteria belonging to Clostridium spp. were the initial colonizers rapidly followed by Bifidobacterium, Bacteroides, Clostridium, Streptococcus, Enterococcus and Actinomyces. Bifidobacterium species appeared already after five days in the breast-fed babies while there was a delay in the baby who received a formula based diet during only one day after birth. In each baby two or three bifidobacterial species including B. infantis were found. The observed variations in species were not associated with the feeding changes. The comparison of DGGE profiles of the babies and their parents patterns showed bands with equal migration suggesting a vertical transmission determined by genetic and environmental factors. The brief appearance of pioneer bacteria determined as being E. coli and Enterococcus spp. in the profile from the baby under antibiotic therapy, was succeeded by a small stable community consisting of Ruminococcus species. No Bifidobacterium sequences were detectable in this antibiotic-treated baby in spite of a partly breast-milk diet.     

Selective plating medium for quantitative recovery of food-borne Listeria monocytogenes

A new plating medium (lithium chloride-ceftazidime agar [LCA]) was designed to quantitatively recover food-borne Listeria monocytogenes in the form of large colonies while inhibiting most other food-borne microorganisms. This medium included brain heart infusion agar as the nutritive agar base and a combination of selective agents (LiCl, glycine anhydride, and ceftazidime). Comparison of LCA and lithium chloride-phenylethanol-moxalactam agar (LPM) indicated that both were equally effective for the enumeration of the cold-tolerant pathogen in artificially and naturally contaminated foods. However, LCA was more effective than LPM in the recovery of sublethally heat-injured cells. Moreover, Listeria colonies on LCA exhibited a more distinct bluish hue than those on LPM when viewed by the Henry oblique transillumination technique.     

Selective plating medium for enumeration and recovery of a hexachlorocyclohexane-degrading Pseudomonas Ptm+ strain from soil

A double selective plating medium has been developed to enumerate a Pseudomonas Ptm+ strain capable of assimilating hexachlorocyclohexane (HCH). The ability of the isolate to utilize HCH and/or streptomycin as sole sources of carbon was chosen to impart selectivity. In trials when serial 10-fold soil dilutions were spread on HCH plus streptomycin mineral agar and incubated, the normal microflora did not grow. When soil containing an HCH degrading Pseudomonas was cultured, only the target colonies developed. This double selective plating method is suitable for environmental monitoring of HCH scavengers as the medium is sensitive, specific and practical.     

Selective plating medium for quantitative recovery of food-borne Listeria monocytogenes.

A new plating medium (lithium chloride-ceftazidime agar [LCA]) was designed to quantitatively recover food-borne Listeria monocytogenes in the form of large colonies while inhibiting most other food-borne microorganisms. This medium included brain heart infusion agar as the nutritive agar base and a combination of selective agents (LiCl, glycine anhydride, and ceftazidime). Comparison of LCA and lithium chloride-phenylethanol-moxalactam agar (LPM) indicated that both were equally effective for the enumeration of the cold-tolerant pathogen in artificially and naturally contaminated foods. However, LCA was more effective than LPM in the recovery of sublethally heat-injured cells. Moreover, Listeria colonies on LCA exhibited a more distinct bluish hue than those on LPM when viewed by the Henry oblique transillumination technique.     

Selective purification and characterization of adiponectin multimer species from human plasma

Adiponectin is an adipocyte-derived hormone and known to form several species of multimer, however, the precise components of each multimer have not been fully determined. We purified each multimer adiponectin selectively from human plasma and characterized them by affinity columns using anti-adiponectin, gelatin, or anti-albumin antibody and gel filtration. We found that adiponectin exists as four species of multimers in human plasma. According to their migrating mobility and N-terminal amino acid analysis, we defined them as a trimer, albumin-binding trimer, hexamer, and HMW. Low pH shifted HMW to hexamer, raising the possibility that HMW is a 12 mer or larger multimer. We also showed that HMW had the highest binding activity to the membrane fractions of C2C12 myocytes and activated AMPK most potently. Our results indicate that adiponectin forms diverse multimer species and at least some of the functional properties are dependent on a multimer status.     

Effect of production conditions on the stability of a human bifidobacterial species Bifidobacterium longum in yogurt

Aims:  Human bifidobacteria are more sensitive to external environmental factors than animal bifidobacteria, and it is difficult to ensure their stable survival in yogurt. The purpose of this investigation was to observe the survival of human bifidobacteria in yogurts produced under various production conditions.
Methods:  Frozen or lyophilized bifidobacteria starters containing Bifidobacterium longum BB536 originally isolated from an infant, and commercial lyophilized yogurt starters were used for yogurt preparation. After producing yogurts under various conditions, the survival of bifidobacteria in these yogurts over various storage periods was observed.
Results:  Although there were some differences in bifidobacterial survival in yogurt between various production conditions, more than 1·0 × 10⁷ CFU g⁻¹ of Bif. longum survived in yogurt after 35 days' storage at 5°C. Lower fermentation temperature (37°C) and inclusion of Lactococcus lactis in the starter significantly ( P  < 0·05) improved survival of Bif. longum in the yogurt.
Conclusion:  In this investigation, the human bifidobacterial strain Bif. longum survived adequately in yogurt, although the fermentation temperature and starter composition affect bifidobacterial survival.
Significance and Impact of the Study:  This investigation indicates that stable probiotic yogurt using human bifidobacteria can be produced by choosing optimal production conditions.     

Distribution of bifidobacterial species in human intestinal microflora examined with 16S rRNA-gene-targeted species-specific primers.

In order to clarify the distribution of bifidobacterial species in the human intestinal tract, a 16S rRNA-gene-targeted species-specific PCR technique was developed and used with DNAs extracted from fecal samples obtained from 48 healthy adults and 27 breast-fed infants. To cover all of the bifidobacterial species that have been isolated from and identified in the human intestinal tract, species-specific primers for Bifidobacterium longum, B. infantis, B. dentium, and B. gallicum were developed and used with primers for B. adolescentis, B. angulatum, B. bifidum, B. breve, and the B. catenulatum group (B. catenulatum and B. pseudocatenulatum) that were developed in a previous study (T. Matsuki, K. Watanabe, R. Tanaka, and H. Oyaizu, FEMS Microbiol. Lett. 167:113-121, 1998). The specificity of the nine primers was confirmed by PCR, and the species-specific PCR method was found to be a useful means for identifying Bifidobacterium strains isolated from human feces. The results of an examination of bifidobacterial species distribution showed that the B. catenulatum group was the most commonly found taxon (detected in 44 of 48 samples [92%]), followed by B. longum and B. adolescentis, in the adult intestinal bifidobacterial flora and that B. breve, B. infantis, and B. longum were frequently found in the intestinal tracts of infants. The present study demonstrated that qualitative detection of the bifidobacterial species present in human feces can be accomplished rapidly and accurately.     

Assessment of species diversity from species abundance distributions at different localities

We show how the spatial structure of species diversity can be analyzed using the correlation between the log abundances of the species in the communities, assuming that two communities at different localities can be described by a bivariate lognormal species abundance distribution. A useful property of this approach is that the log abundances of the species at two localities can be considered as samples from a bivariate normal distribution defined by only five parameters. The variances and the correlation can be estimated by maximum likelihood methods even if there is no information about the sampling intensity and the number of unobserved species. This method also enables estimation of over-dispersion in the sampling relative to a Poisson distribution that allows sampling adjustment of the estimate of β-diversity. Furthermore, we also obtain a partitioning of species diversity into additive components of α-, β- and γ-diversity. For instance, if the correlation between the log abundances of the species is close to one, the same species will be common and rare in the two communities and the β-diversity will be low. We illustrate this approach by analysing similarities of communities of rare and endangered species of oak-living beetles in south-eastern Norway. The number of recorded species was estimated to be only 48.1% of the total number of species actually present in these communities. The correlations among communities dropped rather quickly with distance with a scaling of order 200 km. This illustrates large spatial heterogeneity in species composition, which should be accounted for in the design of schemes of such devices for assessing species diversity in these habitat-types.     

Estimating changes in species abundance from occupancy and aggregation

Predicting the change in abundance is pivotal for evaluating species’ current conservation status and population viability. Empirical works have suggested that species with an increasing abundance have a more aggregated distribution than those with a declining abundance (namely, the change-aggregation hypothesis, CAH). Here we introduced an improved negative binomial distribution model of the occupancy-abundance relationship (OAR) to estimate the change in abundance from changes in occupancy or aggregation. Analysis of the model suggests that (i) in general the change in abundance is synchronized with the change in occupancy when the level of environmental heterogeneity remains constant, and (ii) there could exist a threshold of the population density above which the CAH is no longer valid. Tests using data of epigaeic ants in Fynbos of South Africa collected from different seasons and macro-invertebrates from different localities in streams of central Spain verified these model propositions and thus support the use of this model as a monitoring method for assessing species persistence. Results suggest that the change in abundance can be estimated from the change in occupancy often obtained from cost-efficient presence-absence records, and a revision of the traditional CAH is necessary to capture the threshold phenomenon in the change-aggregation relationship. This work thus signifies the use of the three distinct but related concepts of population structure (i.e. occupancy, abundance and aggregation) in conservation biology.     

Isolation of Methanobrevibacter smithii from human feces.

Fecal specimens from nine adults were examined for the presence of methanogenic bacteria. Enrichment cultures of five specimens produced methane in 5 days. Of these five specimens, three were tested and produced methane during a short-term incubation. Four specimens did not produce methane in either short-term incubation or in enrichment culture. Each methanogenic culture contained methanogens similar in morphology to organisms of the genus Methanobrevibacter and showed factor-420 fluorescence by fluorescence microscopy. Pure cultures were obtained from four of the five methanogenic enrichment cultures. Each isolate grew and formed methane from either H2-CO2 or formate, but growth obtained with formate was poor. None of the isolates used acetate, methanol, or trimethylamine. All isolates grew in the presence of bile salts. In immunological studies, each isolate was closely related to the type strain of Methanobrevibacter smithii, a finding consistent with the physiological and morphological similarities between the isolates and the type strain.     

Simplified method for recovery and PCR detection of Cryptosporidium DNA from bovine feces.

An assay to identify Cryptosporidium DNA in bovine feces has been developed emphasizing standardization of sample preparation and simplification of the DNA recovery process for PCR amplification and DNA hybridization detection. The Cryptosporidium DNA recovery-PCR detection procedure (CR-PCR) can recover DNA suitable for PCR amplification without using or generating hazardous chemicals or wastes. In comparisons with a commercial enzyme-linked immunoassay (Color Vue-Cryptosporidium; Seradyn, Indianapolis, Ind.), the CR-PCR could detect 10(3) to 10(4) times fewer purified oocysts diluted in solution (water or buffered saline) and 10(2) times fewer oocysts from diarrheic feces and showed earlier detectability from solid, nondiarrheic feces in an experimental infection. This assay may prove useful for detecting Cryptosporidium oocysts in feces and in clarifying the role of livestock in waterborne outbreaks of cryptosporidiosis.     

Enumeration and isolation of cellulolytic and hemicellulolytic bacteria from human feces

The fibrolytic microbiota of the human large intestine was examined to determine the numbers and types of cellulolytic and hemicellulolytic bacteria present. Fecal samples from each of five individuals contained bacteria capable of degrading the hydrated cellulose in spinach and in wheat straw pretreated with alkaline hydrogen peroxide (AHP-WS), whereas degradation of the relatively crystalline cellulose in Whatman no. 1 filter paper (PMC) was detected for only one of the five samples. The mean concentration of cellulolytic bacteria, estimated with AHP-WS as a substrate, was 1.2 X 10(8)/ml of feces. Pure cultures of bacteria isolated on AHP-WS were able to degrade PMC, indicating that interactions with other microbes were primarily responsible for previous low success rates in detecting fecal cellulolytic bacteria with PMC as a substrate. The cellulolytic bacteria included Ruminococcus spp., Clostridium sp., and two unidentified strains. The mean concentration of hemicellulolytic bacteria, estimated with larchwood xylan as a substrate, was 1.8 X 10(10)/ml of feces. The hemicellulose-degrading bacteria included Butyrivibrio sp., Clostridium sp., Bacteroides sp., and two unidentified strains, as well as four of the five cellulolytic strains. This work demonstrates that many humans harbor intestinal cellulolytic bacteria and that a hydrated cellulose source such as AHP-WS is necessary for their consistent detection and isolation.     

Urease assay and urease-producing species of anaerobes in the bovine rumen and human feces.

A growth medium and test were developed for rapid detection of urease in fermentative anaerobic bacteria. Using nonselective rumen fluid roll-tube agar medium and the new test, it was confirmed that Peptostreptococcus productus is often the most numerous urease-forming species in human feces. Also, some fecal strains of Ruminococcus albus, Clostridium innocuum, and Clostridium beijerinckii produced urease. Single strains of Fusobacterium prausnitzii, Coprococcus catus, and Streptococcus mitis that were strongly ureolytic on isolation later lost this ability. Urease activity was also detected in many strains of nonselectively isolated rumen species. They include Succinivibrio dextrinosolvens, Treponema sp., Ruminococcus bromii (not previously known to be present in the rumen), Butyrivibrio sp., Bifidobacterium sp., Bacteroides ruminicola, and P. productus. Most P. productus strains contain urease; however, the uniformity of this feature in the other species noted above is not known. The urease in many of these species was not detected if the growth medium contained 0.2% or more (each) yeast extract and Trypticase.     

Oxygen tolerance of anaerobic bacteria isolated from human feces

The large bowel intestinal flora of mammals is made up mostly of O₂-intolerant anaerobic microorganisms which are irreversibly damaged by brief exposure to air. The aim of our work was to investigate the effect of atmospheric O₂ on human intestinal anaerobic microorganisms. Thirty O₂-intolerant bacterial strains that reached 100% mortality after 120 min of air exposure were isolated. Ten of these strains were tested for their atmospheric O₂ sensitivity as a function of air exposure time; all tested microorganisms showed a similar mortality trend on exposure to air. In fact, 50% of cells survive, on the average, after 4–5 min of atmospheric O₂; this percentage decreases to 3–5% after only 20 min, and after 40 min only one cell in a thousand survives; all strains reached 100% mortality in a time range of 100–120 min. The strains examined were identified as belonging to the generaEubacterium, Peptostreptococcus, andCoprococcus.     

Characterization of an O-desmethylangolensin-producing bacterium isolated from human feces

A bacterium that converted daidzein to O-desmethylangolensin was isolated from the feces of healthy humans. It was an obligately anaerobic, nonsporeforming, nonmotile and Gram-positive rod. The isolate used glucose, sucrose, raffinose, maltose, and fructose as carbon sources. It did not hydrolyze gelatin, esculin, or starch. The strain was urease, acid phosphatase, and arginine dihydrolase positive. It was catalase, oxidase, H₂S, and indole negative. The major products of glucose fermentation were butyrate and lactate. Its mol% G+C was 51.2. The major cellular fatty acids were C_16:0 DMA, C_16:0, and C_16:0 aldehyde. The structural type of cell wall peptidoglycan was suggested to be A1γ. The isolate was susceptible to β-lactam, cefem, and macrolide antibiotics and resistant to aminoglycoside and quinolone antibiotics. The bacterium was related to Eubacterium ramulus ATCC29099^T, Eubacterium rectale ATCC33656^T, and species of the genus Roseburia, but the highest 16S rRNA gene similarity to these described species was only 94.4%, consistent with its being classified as a novel genus. Based on the above, the isolate, named strain SY8519, was identified as belonging to a novel genus in the Clostridium rRNA cluster XIVa.     

Isolation of an antigenically unique methanogen from human feces

A methanogenic bacterium with the morphological and physiological properties of the genus Methanobrevibacter was isolated from the feces of a Japanese man who excreted methane in his breath. Indirect immunofluorescence staining revealed that the isolate had an antigenicity unrelated to that of any known members of the genus Methanobrevibacter.     

Enumeration of polysaccharide-degrading Bacteroides species in human feces by using species-specific DNA probes

DNA probes that are specific for each of five predominant species of human colonic Bacteroides (B. thetaiotaomicron, B. uniformis, B. distasonis, "Bacteroides group 3452-A", and B. ovatus) were used to detect and enumerate these species in fecal samples from two adult volunteers. These five species are capable of fermenting many of the complex polysaccharides that are thought to be sources of carbon and energy for bacteria in the colon. Estimates for the concentrations of some of these species in feces have not been previously available because of the difficulties in differentiating colonic Bacteroides spp. by conventional biochemical tests. Our results indicate that all the species except B. ovatus were present in high numbers (greater than 10(9)/g [dry weight]) in the feces of both volunteers. However, the concentrations of the more versatile polysaccharide-degrading species within this group of organisms (7.6 X 10(9) to 12.0 X 10(9)/g [dry weight] for B. thetaiotaomicron; 2.9 X 10(9) to 6.3 X 10(9)/g [dry weight] for "Bacteroides group 3452-A") did not differ significantly from the concentrations of less versatile polysaccharide-degrading species (1.2 X 10(10) to 2.0 X 10(10)/g [dry weight] for B. uniformis; 5.8 X 10(9) to 8.4 X 10(9)/g [dry weight] for B. distasonis). B. ovatus was not detectable by our method. Since our lower limit of detection is approximately 1 X 10(9) to 2 X 10(9)/g (dry weight) of feces, this is consistent with earlier estimates that indicated that the concentration of B. ovatus in feces is near or below this value.(ABSTRACT TRUNCATED AT 250 WORDS)