OBJECTIVETo investigate the composition of bacteria in the stools of infants and the colonization of intestinal microbiota during infancy.

METHODSFresh stools were collected from 15 healthy infants at 0, 2, 4, 7, 10, 14, and 28 days and 3, 6, and 12 months after birth. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) was used to analyze the composition of intestinal microbiota, perform sequencing of dominant bacteria, and to analyze the changes in the composition of intestinal microbiota during infancy.

RESULTSDGGE fingerprint showed that the composition of intestinal microbiota during infancy changed significantly over time after birth. The cloning and sequencing results indicated that Proteobacteria colonized the earliest, mainly the obligate aerobes Enterobacter and Pseudomonas, followed by the obligate anaerobes (Clostridium hathewayi and Veillonella parvula) and the facultative anaerobe Clostridium ramosum in Firmicutes, and Verrucomicrobia. Actinobacteria colonized the latest, mainly Bifidobacterium, and gradually became dominant bacteria.

CONCLUSIONSDuring infancy, obligate aerobes colonize the intestinal tract the earliest, followed by obligate anaerobes and facultative anaerobes. Proteobacteria colonizes the earliest, followed by Firmicutes and Verrucomicrobia, and Actinobacteria, mainly Bifidobacterium, colonizes the latest.

Denaturing Gradient Gel Electrophoresis ; methods ; Feces ; microbiology ; Female ; Gastrointestinal Microbiome ; Humans ; Infant ; Male ; Polymerase Chain Reaction ; methods

Aims: It has been hypothesized that root exudates can be a nutritional factor influencing the bacterial community structure as well as the occurrence of prototrophs and auxotrophs in rhizospheres. The present study was performed to examine the community structures of total bacterial DNA, cultivable bacteria and prototrophs in 3 soil samples with different levels of abundance of root exudates. Methodology and results: Denaturing gradient gel electrophoresis (DGGE) was performed to examine the community structures of total bacterial DNA, cultivable bacteria and prototrophs in 3 soil samples including bulk soil, rhizosphere of a single plant species and rhizosphere of multiple plant species. For clustering analysis, a dendrogram generated from the DGGE patterns revealed the different bacterial community structures in these soil samples. Both rhizospheres claded together, separating from bulk soil. The DGGE patterns of cultivable bacteria showed particular fingerprints corresponding to kinds of media and soil samples. Nutrient agar (NA) medium, isolation medium for prototroph (IMP) and IMP supplemented with soil extracts were used for bacterial cultivations. Prototrophs were isolated and examined by random amplified polymorphic DNA (RAPD) and 16S rRNA gene sequence analysis. The genetic diversity of prototrophs in 3 soil samples was similar (approximately 5% to 10% similarities) and most of them (13 of 28 strains) were members of Pseudomonas with 97% to 100% identities. Conclusion, significance, and impact of study: The present study provides a strong evidence of the influence of root exudates and plant species on bacterial community structures.
Denaturing Gradient Gel Electrophoresis

OBJECTIVETo analyze the differences between the bacterial diversities in the saliva of caries-free and caries-susceptible adolescents through polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE).

METHODSTwenty adolescent subjects aged 12-18 years were recruited and subdivided into two groups: caries-free adolescents (n = 10) and caries-susceptible adolescents (n = 10). Saliva samples were collected. Total DNA was isolated directly from each sample. A portion of the 16S rRNA gene locus was PCR-amplified by using universal primers. Microbial diversity was analyzed through PCR-DGGE.

RESULTSAnalyzing the DGGE profile, we found that the composition of the saliva microbiome exhibited great intra-individual differences; the average band numbers of the caries-free adolescent group and the caries-susceptible adolescent group were 32.5 ± 3.7 and 27.3 ± 3.4, respectively. The differences between the groups were statistically significant (P = 0.008). Shannon-Wiener's indexes of the caries-susceptible adolescent group and the caries-free adolescent group were 2.5 ± 0.2 and 2.6 ± 0.2, respectively, but the differences between the groups were not significant (P = 0.405). Clustering analysis results suggested that most of the samples in the same group clustered together; this observation showed a high community structure similarity.

CONCLUSIONThe microbial diversity and complexity of bacteria in saliva are significantly higher in caries-free adolescents than in caries-susceptible adolescents. During caries development, bacterial diversity in the saliva likely decreases.

Adolescent ; Bacteria ; Child ; DNA, Bacterial ; analysis ; Denaturing Gradient Gel Electrophoresis ; Dental Caries ; microbiology ; Dental Caries Susceptibility ; Humans ; Microbiota ; Mouth ; microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S ; Saliva ; microbiology

The aim of this study was to comprehensively investigate the correlations between foliar fungal endophyte communities and effective components accumulations in Salvia miltiorrhiza. Foliar samples of S. miltiorrhiza were collected in 5 different areas. Their fungal endophyte communities and effective component contents were determined by denaturing gradient gel electrophoresis (DGGE) and high performance liquid chromatography (HPLC), respectively. The results showed that, for characteristics of foliar fungal endophyte communities and effective component contents, there were both similarities and differences among the five samples. Correlation analysis of DGGEs' band and 24 effective components revealed a significant correlations (P < 0.01). For examples, 4 bands (15, 18, 23 and 26) were all significantly correlated with the accumulations of caffeic acid, salvianolic acid B, salvianolic acid C and dihydrotanshinone I.
Chromatography, High Pressure Liquid ; Cluster Analysis ; Denaturing Gradient Gel Electrophoresis ; Endophytes ; chemistry ; Fungi ; chemistry ; Salvia miltiorrhiza ; chemistry ; microbiology

This study aims to analyze and compare the effect of cell wall-broken decoction pieces, conventional decoction pieces and conventional powder of Rhodiolae Crenulatae Radix et Rhizoma on the intestinal flora of normal mice. The conventional bacterial culture and PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) were adopted for the mice after the oral administration for 14 days. According to the bacterial culture results, the 1/8 dose cell wall-broken decoction pieces group showed fewer Enterococcus and Escherichia coli bacillus but more Lactobacillus and Bifidobacterium than the conventional decoction pieces group and the traditional powder group (P <0.05). Meanwhile, on the basis of the PCR-DGGE results, the 1/8 dose cell wall-broken decoction pieces group revealed the highest Shannon-Wiener index (H) and species richness (S) among the seven groups, with extremely significant differences compared with the normal group (P <0.01), significant differences compared with the conventional decoction pieces group and the conventional powder group (P <0.05) and a high intra-group similarity. In conclusion, the long-term intake of 1/8 dose Rhodiolae Crenulatae Radix et Rhizoma cell wall-broken decoction pieces showed a certain effect in regulating intestinal tract by promoting the growth of Lactobacillus and Bifidobacterium. Furthermore, the intestinal flora community will become more stable.
Animals ; Bifidobacterium ; drug effects ; genetics ; growth & development ; Cell Wall ; Denaturing Gradient Gel Electrophoresis ; Intestines ; microbiology ; Lactobacillus ; drug effects ; genetics ; growth & development ; Mice ; Mice, Inbred C57BL ; Polymerase Chain Reaction ; Rhizome ; Rhodiola

In order to reveal the cause of disease occurred in the process of Coptis chinensis growth, this paper studied the bacterial species diversity index of different aged rhizospheric and non-rhizospheric soil planting normal or sick C. chinensis by using PCR-DGGE technique. The representative DGGE bands were chosen to be cloned, and sequenced, the phylogeny were constructed. The results showed that the bacterial communities were very different between the normal and diseased soil samples of C. chinensis, and the diversity index (H) of diseased soil samples were higher than that of normal soil samples. Sequencing analysis of representative cloned DGGE bands showed that the unculturable bacteria were the dominant groups, and bacteria belonged to genus Bacillus, Acidovorax, Acinetobacter, uncultured Kluyvera, and uncultured Comamonas were also existing, but the reported plant pathogenic bacteria were not found in the C. chinensis planting soil. The density and brightness of clone band d in diseased soil samples was higher than that in normal soil sample, and sequencing analysis showed that it belonged to genus Acidovorax. Obviously, during the process of C. chinensis growth, the rhizospheric bacteria population changed, and the quantity of bacteria belong Acidovorax increased, which probably resulted in the disease occurred during C. chinensis growth.
Bacteria ; classification ; genetics ; isolation & purification ; Biodiversity ; Coptis ; growth & development ; microbiology ; Denaturing Gradient Gel Electrophoresis ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Rhizosphere ; Soil Microbiology

Among solute carrier proteins, the organic anion transporters (OATs) play an important role for the elimination or reabsorption of endogenous and exogenous negatively charged anionic compounds. Among OATs, SLC22A9 (hOAT7) transports estrone sulfate with high affinity. The net decrease of estrogen, especially in post-menopausal women induces rapid bone loss. The present study was performed to search the SNP within exon regions of SLC22A9 in Korean females with osteoporosis. Fifty healthy controls and 50 osteoporosis patients were screened for the genetic polymorphism in the coding region of SLC22A9 using GC-clamped PCR and denaturing gradient gel electrophoresis (DGGE). Six SNPs were found on the SLC22A9 gene from Korean women with/without osteoporosis. The SNPs were located as follows: two SNPs in the osteoporosis group (A645G and T1277C), three SNPs in the control group (G1449T, C1467T and C1487T) and one SNP in both the osteoporosis and control groups (G767A). The G767A, T1277C and C1487T SNPs result in an amino acid substitution, from synonymous vs nonsynonymous substitution arginine to glutamine (R256Q), phenylalanine to serine (F426S) and proline to leucine (P496L), respectively. The Km values and Vmax of the wild type, R256Q, P496L and F426S were 8.84, 8.87, 9.83 and 12.74 microM, and 1.97, 1.96, 2.06 and 1.55 pmol/oocyte/h, respectively. The present study demonstrates that the SLC22A9 variant F426S is causing inter-individual variation that is leading to the differences in transport of the steroid sulfate conjugate (estrone sulfate) and, therefore this could be used as a marker for certain disease including osteoporosis.
Amino Acid Substitution ; Arginine ; Avena ; Carrier Proteins ; Clinical Coding ; Denaturing Gradient Gel Electrophoresis ; Estrogens ; Estrone ; Exons ; Female ; Glutamine ; Humans ; Leucine ; Organic Anion Transporters ; Osteoporosis* ; Phenylalanine ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Polymorphism, Single Nucleotide ; Proline ; Serine

OBJECTIVETo analyze the differences between the oral microbiota of monozygotic and dizygotic twins by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE).

METHODSA total of 20 pairs of twin children were included in this study, in which 10 pairs were monozygotic (MZ) twins, and 10 pairs were dizygotic (DZ) twins. Of the 20 pairs, 10 pairs of twins had primary dentition, and 10 pairs had mixed dentition; 17 children had caries, and 23 children had no caries. Genomic DNA was extracted from saliva samples. The 16s rRNA was amplified and analyzed by PCR-DGGE. The PCR-DGGE band number and Shannon index were calculated.

RESULTSCluster analysis showed high similarity in the oral bacterial community seen in co-twins. However, no significant difference was seen between MZ and DZ twins. In the primary dentition, the PCR-DGGE band number and Shannon index of children with caries (11.00 +/- 1.56, 1.05 +/- 0.36) were lower than those of children without caries (14.00 +/- 2.74, 1.44 +/- 0.37) (P < 0.05). In mixed dentition, the PCR-DGGE band number and Shannon index of children with caries (11.88 +/- 4.05, 1.18 +/- 0.36) were lower than those of children without caries (14.31 +/- 5.71, 1.28 +/- 0.47), but the differences were not statistically significant (P > 0.05).

CONCLUSIONEnvironmental factors may have a stronger effect on the constitution of oral microbiota in children compared with genetic factors. Children without caries may have a richer microbial diversity compared with children with caries.

Bacteria ; Child ; Denaturing Gradient Gel Electrophoresis ; Dental Caries ; Female ; Humans ; Male ; Microbiota ; Mouth ; microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S ; Saliva ; Twins, Monozygotic

OBJECTIVETo research the diversity of endophytic fungal communities among Ligusticum chuanxiong growing at 5 areas in Sichuan province, and illuminate the developing mechanism of geoherbs from the microecological perspective.

METHODThe PCR-DGGE and DNA sequencing techniques were used to analyze the endophytic fungi community of L. chuanxiong.

RESULTThe community of endophytic fungi present difference among different growing areas. Though minor difference were found among individuals at the same area, similarity among individuals from the same growing areas were higher significantly than those from different growing areas. Compared with the other 4 growing areas, L. chuanxiong from Shiyang town, Dujiangyan city had more abundant endophytic fungi and low similarity to others, and which probably had special types of fungi.

CONCLUSIONThe abundant and stable endophytic fungal community is an important factor for the development of geoherb L. chuanxiong at Shiyang town, Dujiangyan city.

Denaturing Gradient Gel Electrophoresis ; methods ; Ligusticum ; genetics ; growth & development ; Polymerase Chain Reaction ; methods ; Sequence Analysis, DNA

OBJECTIVEThe catheter-related infections caused by mechanical ventilation have become a intractable clinical problem, and it is related to the formation of bacterial biofilm (BF) on the surface of the implanted material. The majority of natural biofilms are formed by multiple bacterial species. However, there always only one or limited species were detected on tracheal tubes removed from intubated neonates by using traditional methods including bacterium culture and antigen detection. The aims of this study were to observe the bacterial communities diversity of BF on endotracheal tube (ETT), and discuss the difference between traditional bacterium culture methods and the use of molecular biology techniques on the basis of denatured gradient gel electrophoresis (DGGE), to provide new ideas for clinical prevention, diagnosis and treatment of bacterial infections.

METHODThirty-five ETTs were obtained from 26 neonates on mechanical ventilator (from October 2012 to March 2013) in Department of Neonatology of Children's Hospital. Among the patients, 18 were boys and 8 girls, and 19 patients were < 37 weeks gestational age and 7 patients ≥ 37 weeks. DGGE profiling of 16S rDNA gene amplicons was used to assess the diversity of the bacterial population by using the software of quantity one. TA Cloning Kit and sequencing were used to investigate the distribution of bacteria and common dominant bacteria in ETT-BF.

RESULTThe mean bands of 35 ETTs cases were 13.8 ± 5.4 from 16S rDNA PCR-DGGE, and the mean Shanon-Wiener indexes was 2.42 ± 0.38. The 16 ETTs were collected in different stages of diseases from the 7 patients. The indwelling days of 6/7 patients' ETTs increased, the Shanon-siener indexes were decreased. Among the 6 cases from different basic illnesses, and there were different Shanon-siener indexes. The result of molecular cloning and sequencing for 24 dominant bands showed that 35 cases (100%) contained Klebsiella SP·, 28 cases (80%) had Pseudomonas SP·, 27 cases (77%) had Streptococcus SP·, and 32 cases (91%) had Uncultured bacterium, while more than 2 bacterial species were found in 34 cases (97%). 28/35 (80%) Klebsiella SP· and 22/27(82%) Streptococcus SP· were accompanied by Pseudomonas SP·. There were 22 positive results of sputum culture from 26 newborns, including 10 strains (45%) of Klebsiella pneumoniae, 2 strains (9%) of Acinetobacter baumannii, Enterobacter cloacae and non-cultured bacterium in each patient (5%), but only one bacterium isolated from every sputum. Eight sputum samples had normal flora only, corresponding to the ETTs on which Klebsiella and other bacterial genuses were found.

CONCLUSIONThe diversity of microbiota in BF on ETT was confirmed. 16S rDNA PCR-DGGE could produce a more complete picture of bacterial community than traditional bacterium culture method. Klebsiella, Pseudomonas and Streptococcus were common dominant bacteria in ETT-BF, and there might be interactions among them in the formation of BF.

Bacteria ; classification ; genetics ; isolation & purification ; Biodiversity ; Biofilms ; Catheter-Related Infections ; microbiology ; DNA, Bacterial ; analysis ; genetics ; Denaturing Gradient Gel Electrophoresis ; Female ; Humans ; Infant, Newborn ; Intubation, Intratracheal ; adverse effects ; Klebsiella ; genetics ; isolation & purification ; Male ; Polymerase Chain Reaction ; Pseudomonas ; genetics ; isolation & purification ; RNA, Ribosomal, 16S ; genetics ; Respiration, Artificial ; adverse effects ; Sputum ; microbiology ; Streptococcus ; genetics ; isolation & purification ; Ventilators, Mechanical ; microbiology