New Strategies for Cultivation and Detection of Previously Uncultured Microbes

An integrative approach was used to obtain pure cultures of previously uncultivated members of the divisions Acidobacteria and Verrucomicrobia from agricultural soil and from the guts of wood-feeding termites. Some elements of the cultivation procedure included the following: the use of agar media with little or no added nutrients; relatively long periods of incubation (more than 30 days); protection of cells from exogenous peroxides; and inclusion of humic acids or a humic acid analogue (anthraquinone disulfonate) and quorum-signaling compounds (acyl homoserine lactones) in growth media. The bacteria were incubated in the presence of air and in hypoxic (1 to 2% O₂ [vol/vol]) and anoxic atmospheres. Some bacteria were incubated with elevated concentrations of CO₂ (5% [vol/vol]). Significantly more Acidobacteria were found on isolation plates that had been incubated with 5% CO₂. A simple, high-throughput, PCR-based surveillance method (plate wash PCR) was developed. This method greatly facilitated detection and ultimate isolation of target bacteria from as many as 1,000 colonies of nontarget microbes growing on the same agar plates. Results illustrate the power of integrating culture methods with molecular techniques to isolate bacteria from phylogenetic groups underrepresented in culture.     

Isolation and identification of fecal bacteria from adult swine.

An examination of the fecal microflora of adult swine was made with regard to the efficiency of several roll tube media in enumeration and recovery of anaerobes, the effects of medium constituents on recovery, and the isolation and identification of the predominant kinds of bacteria. Total number of organisms by microscopic bacterial counts varied among fecal samples from 4.48 X 10(10) to 7.40 X 10(10) bacteria/g (wet weight). Comparison of different nonselective roll tube media indicated that about 30% of the fecal bacteria could be recovered with a rumen fluid (40%, vol/vol) medium (M98-5). Recoveries of 21 and 15%, respectively, were obtained with M10 and rumen fluid-glucose-cellobiose agar (RGCA) media. Rumen fluid, Trypticase, sugars, and CO2 gas phase were important components required for maximum recovery with this medium. Similar high recoveries of anaerobes were also obtained with M98-5 containing swine cecal extract of place in rumen fluid or M10 plus swine cecal extract. Significantly lower recoveries were observed with RCGA, media supplemented with swine fecal extracts, reinforced clostridial medium, brain heart infusion agar, and prereduced blood agar. Ninety percent of the bacteria isolated from roll tube media were gram positive and consisted of facultatively anaerobic streptococci, Eubacterium sp., Clostridium sp., and Propionibacterium acnes. The remainder of the flora (8%) included several other species of anaerobes and Escherichia coli. Rumen fluid (or volatile fatty acids), Trypticase, and yeast extract additions to basal media stimulated the growth of anaerobic strains. Variation in the relative proportions of the predominant fecal microflora was observed. This work indicates that satisfactory enumeration, isolation and cultivation of the predominant microflora in swine feces can be obtained when strict anaerobic culture methods and a rumen fluid medium are used.     

Selection of Media for the Isolation of Common Bacterial L-Phase Organisms from a Clinical Specimen

The L-phase of 13 bacteria commonly associated with disease were induced by penicillin and inoculated into various solid and broth media; their growth was recorded for a period of 14 days. Plates containing highly purified agar and sucrose as the stabilizing agent and those incubated under aerobic conditions gave the best results. Magnesium seems to be necessary for growth in broth media on primary isolation, although it may not be necessary on multiple transfers after a more stable state has been reached. Growth in broth media is much more difficult to achieve. Reversion is aided by using a higher concentration of agar in plates, by decreasing the sucrose concentration, and by omitting the antibiotics and horse serum. A procedure has been outlined for the routine culture and identification of L-phase organisms from a clinical specimen.     

Rapid Screen for Bacteria Degrading Water-Insoluble, Solid Hydrocarbons on Agar Plates

A rapid procedure was devised for detecting on solid media bacteria able to degrade water-insoluble, solid hydrocarbons such as the polycyclic aromatic hydrocarbons phenanthrene, anthracene, and biphenyl. After Alcaligenes faecalis AFK2 was inoculated on a plate containing mineral salts agar, an ethereal solution of phenanthrene (about 10%, wt/vol) was sprayed on the surface of the plate, and the plate was incubated at 30°C for 2 to 3 days. Colonies showing degradation were surrounded with clear zones on the opaque plate. A similar clear zone also was formed around colonies which had been grown on a succinate-mineral salts agar or nutrient agar, followed by spraying of the ethereal solution of phenanthrene and further incubating for 1 day. Other phenanthrene-assimilating bacteria, including Beijerinckia Bwt and Pseudomonas SPM64, also formed clear zones on phenanthrene-covered agar plates. This method was applicable to detection of bacteria able to assimilate anthracene, naphthalene, and biphenyl.     

Evaluation of kappa carrageenan as a substitute for agar in microbiological media

Seventy-one samples of the colloid kappacarrageenan extracted from 12 seaweed species were subjected to a number of standard physical demands of solid bacteriological culture media. All samples had a lower melting temperature (less than 67° C) than agar and a gelling (setting) temperature between 16° C and 51° C, some the same and others lower or higher than agar. Temperature spreads were narrow (ca 10° C) to broad (ca 30° C), depending on the seaweed source, but none were as broad as that of agar (ca 40° C). The majority of commercially prepared samples held a slant when incubated at 37° C, but California seaweed colloids were best at 28° C in this test. The majority of samples released little to no water of syneresis in slant tests as well as in plates. Some plates prepared with the colloid were crystal clear as compared to agar plates. All test microorganisms grew as well on kappa-carrageenan media as on agar media. Some media responses could be attributable to the seaweed species, but others could be traced to chemical extraction methods and modification of the colloid.     

Rapid radiometric method for detection of Salmonella in foods.

A radiometric method for the detection of Salmonella in foods has been developed which is based on Salmonella poly H agglutinating serum preventing Salmonella from producing 14CO2 from [14C]dulcitol. The method will detect the presence or absence of Salmonella in a product within 30 h compared to 4 to 5 days by routine culture methods. The method has been evaluated against a routine culture method using 58 samples of food. The overall agreement was 91%. Five samples negative for Salmonella by the routine method were positive by the radiometric method. These may have been false positives. However, the routine method may have failed to detect Salmonella due to the presence of large numbers of lactose-fermenting bacteria which hindered isolation of Salmonella colonies on the selective agar plates.     

Characteristic of clinical strains of gram-negative obligate anaerobes

The aim of the study was to assess prevalence and antibiotic susceptibility profiles ofGram-negative strictly anaerobic bacteria isolated from clinical specimens taken from hospitalized patients in 2005-2006. Biochemical identification and antibiotic susceptibility were done in an automated system ATB Expression (bioMerieux sa). From 12262 specimens examined 867 strains of obligate anaerobes were isolated. Gram-negative strictly anaerobic bacteria were cultured in number of 138 strains (15,9%). All cultures were performed on Columbia agar and Schaedler agar media (bioMerieux sa) supplemented with 5% sheep blood and incubated at 37 degrees C for 48-120 h in 85% N2, 10% H2, 5% CO2. Most frequently isolated was Bacteroides spp. (41,3%). For this group beta-lactamase activity was evaluated by using nitrocefin disc test (Cefinase BBL, Becton Dickinson and Co., Cockeysville, MD, USA). Production of ESBLs was detected with the use of two disc diffusion methods: the double-disc synergy test (DDST) according to Jarlier et al. and the diagnostic disc (DD) test according to Appleton. ESBLs were produced by 5,3% strains of Bacteroides spp. For all Bacteroides spp. strains MIC values were determined by gradient diffusion method Etest (AB BIODISK, Sweden). ESBLs and MIC were performed on Wilkins-Chalgren solid medium supplemented with 5% sheep blood (Difco Lab., USA) and all plates were incubated at 35 degrees C for 48 hours in 85% N2, 10% H2, 5% CO2. Most Gram-negative obligate anaerobes isolated from clinical specimens are still susceptible to imipenem (100%), metronidazole (99,3%) and beta-lactam antibiotics with beta-lactamase inhibitors: piperacillin/tazobactam (99,3%), ticarcillin/clavulanate (99.3%), amoxicillin/clavulanate (97.8%).     

Isolation of novel bacteria, including a candidate division, from geothermal soils in New Zealand

We examined bacterial diversity of three geothermal soils in the Taupo Volcanic Zone of New Zealand. Phylogenetic analysis of 16S rRNA genes recovered directly from soils indicated that the bacterial communities differed in composition and richness, and were dominated by previously uncultured species of the phyla Actinobacteria , Acidobacteria , Chloroflexi , Proteobacteria and candidate division OP10. Aerobic, thermophilic, organotrophic bacteria were isolated using cultivation protocols that involved extended incubation times, low-pH media and gellan as a replacement gelling agent to agar. Isolates represented previously uncultured species, genera, classes, and even a new phylum of bacteria. They included members of the commonly cultivated phyla Proteobacteria , Firmicutes , Thermus/Deinococcus , Actinobacteria and Bacteroidetes , as well as more-difficult-to-cultivate groups. Isolates possessing < 85% 16S rRNA gene sequence identity to any cultivated species were obtained from the phyla Acidobacteria , Chloroflexi and the previously uncultured candidate division OP10. Several isolates were prevalent in 16S rRNA gene clone libraries constructed directly from the soils. A key factor facilitating isolation was the use of gellan-solidified plates, where the gellan itself served as an energy source for certain bacteria. The results indicate that geothermal soils are a rich potential source of novel bacteria, and that relatively simple cultivation techniques are practical for isolating bacteria from these habitats.     

Improving the success of culturing Helicobacter pylori from gastric biopsies

Factors influencing the successful isolation of Helicobacter pylori from human gastric biopsies were studied. Within 24 h, each of the gastric biopsies was inoculated onto chocolate blood agar media and incubated for up to 2 weeks. Among 63 (70%) culture positive cases in 90 patients, 58 (64%) cases were culture positive for both specimens, while five (6%) cases were culture positive in only one biopsy. Of the 63 positive cultures, 51 H. pylori strains (81%) grew on both media with and without antibiotics. Eight strains (13%) grew only on medium without antibiotics, while four isolates (6%) were obtained only from medium with antibiotics. These results support the previous histological observation of patchy colonization of H. pylori in the stomach. The success rate for culture of H. pylori from gastric biopsies increased when two biopsies were taken and inoculated on chocolate blood agar media with and without antibiotics.     

In Vitro Culture of Previously Uncultured Oral Bacterial Phylotypes

Around a third of oral bacteria cannot be grown using conventional bacteriological culture media. Community profiling targeting 16S rRNA and shotgun metagenomics methods have proved valuable in revealing the complexity of the oral bacterial community. Studies investigating the role of oral bacteria in health and disease require phenotypic characterizations that are possible only with live cultures. The aim of this study was to develop novel culture media and use an in vitro biofilm model to culture previously uncultured oral bacteria. Subgingival plaque samples collected from subjects with periodontitis were cultured on complex mucin-containing agar plates supplemented with proteose peptone (PPA), beef extract (BEA), or Gelysate (GA) as well as on fastidious anaerobe agar plus 5% horse blood (FAA). In vitro biofilms inoculated with the subgingival plaque samples and proteose peptone broth (PPB) as the growth medium were established using the Calgary biofilm device. Specific PCR primers were designed and validated for the previously uncultivated oral taxa Bacteroidetes bacteria HOT 365 and HOT 281, Lachnospiraceae bacteria HOT 100 and HOT 500, and Clostridiales bacterium HOT 093. All agar media were able to support the growth of 10 reference strains of oral bacteria. One previously uncultivated phylotype, Actinomyces sp. HOT 525, was cultivated on FAA. Of 93 previously uncultivated phylotypes found in the inocula, 26 were detected in in vitro-cultivated biofilms. Lachnospiraceae bacterium HOT 500 was successfully cultured from biofilm material harvested from PPA plates in coculture with Parvimonas micra or Veillonella dispar/parvula after colony hybridization-directed enrichment. The establishment of in vitro biofilms from oral inocula enables the cultivation of previously uncultured oral bacteria and provides source material for isolation in coculture.     

Chemolithoautotrophic assimilation of dinitrogen by Streptomyces thermoautotrophicus UBT1: identification of an unusual N2-fixing system.

Streptomyces thermoautotrophicus UBT1, which was isolated previously from a burning charcoal pile, was shown to utilize N2 as a sole nitrogen source when growing chemolithoautotrophically with CO or H2 plus CO2 under aerobic conditions at 65 degrees C. Doubling times under diazotrophic conditions were 10 h. S. thermoautotrophicus is a new CO- or H2-oxidizing, obligately chemolithoautotrophic, thermophilic, free-living, aerobic, N2-fixing streptomycete. Its ability to fix N2 was also evident from (i) the incorporation of substantial amounts of 15N2 (about 13%) into cell material, (ii) the formation of H2 during diazotrophic growth, (iii) the repression of 15N2 assimilation and H2 formation by ammonia, and (iv) culture growth yields with N2 as a nitrogen source that were significantly higher than those without any added nitrogen compounds (ca. 2.4 versus < 0.1 mg [dry weight]). The N2-fixing system of S. thermoautotrophicus exhibited several properties not apparent in the diazotrophic bacteria studied so far, since it was (i) incapable of reducing acetylene to ethylene or ethane and (ii) resistant to inhibition by acetylene or ethylene (5% [vol/vol] each), CO (40 to 70% [vol/vol]), or H2 (40% [vol/vol]). Under stringent conditions, nifH and nifDK gene probes from Klebsiella pneumoniae did not hybridize with total DNA from S. thermoautotrophicus.     

Efficacy of artificial humic acid as a selective nutrient in HV agar used for the isolation of soil actinomycetes

The efficacies of various kinds of humic acid, as the source of carbon and nitrogen in HV agar reported in the previous paper, were compared to the selective isolation of soil actinomycetes. The 4 types of natural humic acid, A, B, P and Rp were prepared from different soils, and 3 kinds of artificial humic acid were made from carbohydrates and urea in our laboratory.Among the natural humic acids, type Rp, which has been reported to be associated with an initial state of humification in natural conditions, showed the greatest efficacy.However, one of the artificial humic acids, which was prepared from glucose and urea, was considered to be superior to the Rp natural humic acid: 1) The HV agar containing this artificial humic acid (HV-glucose HA agar) produced the same large number of actinomycete colonies on the plate as that of the HV agar with type Rp soil humic acid (HV-Rp agar). 2) The HV-glucose HA agar restricted the number of bacterial colonies on the plates to one-half of that on HV-Rp agar plates. 3) The quality of natural himic acids varies, whereas artificial ones are more constant and can be made in any laboratory.     

Sensitization of oral bacteria to killing by low-power laser radiation

Twenty-seven compounds were screened for their ability to sensitize Streptococcus sanguis to killing by light from a 7.3-mW Helium/Neon (HeNe) laser. Bacteria were mixed with various concentrations of the test compounds, spread over the surfaces of agar plates, and then exposed to light from the HeNe laser for various time periods. The plates were then incubated and examined for zones of inhibition. Those compounds found to be effective photosensitizers were then tested against Porphyromonas gingivalis, Actinobacillus actinomycetemcomitans, and Fusobacterium nucleatum. Toluidine blue O, azure B chloride, and methylene blue at concentrations of 0.005% (wt/vol) were effective photosensitizers of all four species, enabling killing of bacteria following exposure to laser light for only 30 s.     

A simple method for counting Staphylococcus aureus in swimming pool water

Staphylococcus aureus counts from swimming pool water were determined by the membrane filtration technique. Water samples were passed through a membrane filter and then put on Baird-Parker media. After incubation, the filters were transferred to nutrient agar, and incubated at 37 degrees C, for 3 h. After removal of the filters, the plates were incubated at 60 degrees C for 2 h. An overlay of toluidine blue agar was added and the plates reincubated for 4 h at 37 degrees C. The formation of thermonuclease correlated with the formation of coagulase, and the results indicated that Staphylococcus aureus could be present in swimming pool water without the presence of either coliform or faecal coliform bacteria.     

Selective and Differential Media for Isolation and Tentative Identification of Each Species of Pityrosporum Residing on Normal or Diseased Human Skin

Selective and differential media were designed for each species of Pityrosporum; P. pachydermatis, P. ovale, and P. orbiculare in order to make feasible a quantitative cultivation. Medium for P. pachydermatis (medium A) was composed of 1% trypticase peptone (BBL), 0.5% yeast extract (BBL), 0.3% glucose, 0.2% NaCl, 1.2% KH₂ PO₄ (anhydrous), 1.5% agar, 0.01% ampicillin, and 0.025% cycloheximide with a pH of 5.5. Medium for P. ovale (medium B) was medium A supplemented with 0.05% sodium acetate (anhydrous), 0.2% Tween 80, and 0.025% (selective medium) or 0.075% (differential medium) sodium laurate. Medium for P. orbiculare was medium B (devoid of laurate) supplemented with 2% olive oil, 0.25% glycerol, 0.25% gall powder, 0.05% sodium palmitate, 0.05% sodium stearate, 0.05% sodium oleate and 8% (selective medium) or 10% (differential medium) sodium lactate and an increase in Tween to 1%. For isolation of Pityrosporum, specimens were suspended in 0.1% Tween 80 solution and inoculated onto agar plates of three selective media. The plates were incubated aerobically at 37 C for 8–10 days under conditions of prevention of water loss from the media. The plating efficiency of each selective medium, expressed as a ratio of cultural counts to microscopic counts was generally over 70%. Species of Pityrosporum could also be identified when we inoculated the cell suspension onto differential agar plates and incubated the preparations at 37 C for 7 days.     

In vitro explant culture of mantle epithelium of freshwater pearl mussel

The in vitro culture of nacre secreting pallial mantle explants of freshwater pearl producing mussel, Lamellidens marginalis (Lamarck) included depuration of pearl mussels with different physical and chemical agents to eradicate various commensals, removal of pallial mantle ribbon, aseptic preparation of explants from the ribbon and transfer of those explants into tissue culture petri dishes. Special synthetic tissue culture media enriched with additives viz., inactivated calf fetal serum and antibiotics were poured into plates with explants. The culture plates were incubated at 30 degrees C in a CO2 incubator at 5%, CO2. The cultures could be maintained for 42-45 days without any contamination. After 12 hr epithelial like cells began to migrate out and formed a complete cell sheet surrounding the explant within 12-15 days. The epithelial cells in the culture indicated functional viability as subsequently after 38-40 days of culture, typical aragonitic 'nacre' crystals of CaCO3 could be observed throughout the culture plates.     

Detection of Lactobacillus acidophilus in Feces of Humans, Pigs, and Chickens

Lactobacilli in fecal material from humans, pigs, and chickens were enumerated on lactobacillus selective agar (LBS). In all samples, higher numbers of lactobacilli were detected when plates were incubated in a system flushed with CO₂ rather than in air. Much higher numbers of bacteria from human feces were detected when the LBS agar plates were incubated anaerobically in a hydrogen-carbon dioxide atmosphere (GasPak) than when incubated in CO₂. The bacteria from human feces isolated on LBS agar incubated anaerobically were predominately bifidobacteria. Cultures from all three sources isolated on LBS agar incubated under CO₂ were lactobacilli, including Lactobacillus acidophilus. Differences were observed in biochemical characteristics of some of the L. acidophilus isolated from all three sources. Guanine plus cytosine base ratios of deoxyribonucleic acid isolated from L. acidophilus cultures from humans were lower, in most cases, than those from pigs and chickens.     

Multiple approaches to enhance the cultivability of bacteria associated with the marine sponge Haliclona (gellius) sp

Three methods were examined to cultivate bacteria associated with the marine sponge Haliclona (gellius) sp.: agar plate cultures, liquid cultures, and floating filter cultures. A variety of oligotrophic media were employed, including media with aqueous and organic sponge extracts, bacterial signal molecules, and siderophores. More than 3,900 isolates were analyzed, and 205 operational taxonomic units (OTUs) were identified. Media containing low concentrations of mucin or a mixture of peptone and starch were most successful for the isolation of diversity, while the commonly used marine broth did not result in a high diversity among isolates. The addition of antibiotics generally led to a reduced diversity on plates but yielded different bacteria than other media. In addition, diversity patterns of isolates from agar plates, liquid cultures, and floating filters were significantly different. Almost 89% of all isolates were Alphaproteobacteria; however, members of phyla that are less commonly encountered in cultivation studies, such as Planctomycetes, Verrucomicrobia, and Deltaproteobacteria, were isolated as well. The sponge-associated bacteria were categorized into three different groups. The first group represented OTUs that were also obtained in a clone library from previously analyzed sponge tissue (group 1). Furthermore, we distinguished OTUs that were obtained from sponge tissue (in a previous study) but not from sponge isolates (group 2), and there were also OTUs that were not obtained from sponge tissue but were obtained from sponge isolates (group 3). The 17 OTUs categorized into group 1 represented 10 to 14% of all bacterial OTUs that were present in a large clone library previously generated from Haliclona (gellius) sp. sponge tissue, which is higher than previously reported cultivability scores for sponge-associated bacteria. Six of these 17 OTUs were not obtained from agar plates, which underlines that the use of multiple cultivation methods is worthwhile to increase the diversity of the cultivable microorganisms from sponges.     

九龙江口沉积物TCBS(Thiosulfate Citrate Bile Salts Sucrose)菌群的分布

【目的】调查九龙江流域对厦门海域潜在的病原菌"污染",为相关侵染性病害的预防和控制提供有价值的资料。【方法】通过TCBS(Thiosulfate Citrate Bile Salts Sucrose)培养基从九龙江河口沉积物中分离到158株细菌,应用16S rRNA基因-RFLP(限制性酶切图谱多样性分析)及16S rRNA基因序列分析等方法对158株细菌进行分子鉴定。【结果】研究结果表明九龙江口沉积物中分布的TCBS菌群分别属于7个属,其中假单胞菌属(Pseudomonas)占28%,气单胞菌属(Aeromonas)占24%,假交替单胞菌属(Pseudoalteromonas)占19%,希瓦氏菌属(Shewanella)占13%,芽孢杆菌属(Bacillus)占11%,弧菌属(Vibrio)占4%,嗜冷杆菌属(Psychrobacter)占1%。不同站位TCBS菌群的组成及各菌群的相对差异明显,其中上游区域以非嗜盐或耐盐细菌为主,下游区域以嗜盐细菌和耐盐细菌为主,具有典型的河口细菌分布特征。盐度对各TCBS菌群的分布具有重要的影响。弧菌在整个河口区所占的比例不大(6%-19%)且集中在下游区域。【结论】九龙江口存在大量的条件致病菌,其中以气单胞菌属为代表的耐盐菌,对厦门海域存在陆源性污染的风险;绝大多数弧菌属于海洋土著细菌,正常情况下(非流行性弧菌病期间)非来源于九龙江冲淡水的直接污染。     

Isolation and enumeration of Campylobacter jejuni from poultry products by a selective enrichment method

A direct selective enrichment procedure was developed for the isolation of Campylobacter jejuni from poultry products. The selective enrichment medium (ATB) consisted of (per liter) tryptose (20 g), yeast extract (2.5 g), sodium chloride (5 g), FBP supplement (ferrous sulfate [0.25 g], sodium metabisulfite [0.25 g], sodium pyruvate [0.25 g]), bicine (10 g), and agar (1 g). Hematin solution (6.25 ml; prepared by dissolving 0.032 g of bovine hemin in 10 ml of 0.15 N sodium hydroxide solution and autoclaving at 0.35 kg/cm2 for 30 min), rifampin (25 mg), cefsulodin (6.25 mg), and polymyxin B sulfate (20,000 IU) were added after the medium was sterilized. The pH was adjusted to 8.0. Samples were enriched in the above medium at 42 degrees C for 48 h under an atmosphere of 5% O2, 10% CO2, and 85% N2. Enrichment cultures were streaked on a plating medium composed of Brucella agar, hematin solution, FBP supplement, and the above antibiotics. Plates were incubated under the same conditions as above. Suspect colonies from the plates were confirmed to be C. jejuni by morphological examination, growth characteristics, and biochemical tests. The above method yielded 25 isolates of C. jejuni from 50 samples of retail cut-up chicken and chicken parts, whereas a more complex method involving filtration, centrifugation, selective enrichment under a flowing atmosphere, and membrane filtration yielded only 6 positives from the same samples. The new isolation procedure was particularly effective in isolating C. jejuni in the presence of large numbers of Pseudomonas aeruginosa.(ABSTRACT TRUNCATED AT 250 WORDS)