ERIC-PCR fingerprinting-based community DNA hybridization to pinpoint genome-specific fragments as molecular markers to identify and track populations common to healthy human guts

Inhibition Mechanism of Water-Soluble Chitosan-Curdlan Composite Coating on the Postharvest Pathogens of Serratia marcescens and Pseudomonas syringae in Cherry Tomatoes

Cherry tomatoes, a very popular fruit, are highly susceptible to microbial infestation, which cause significant economic losses. In order to preserve cherry tomatoes better, we treat them with a Chitosan (CTS) and Curdlan (CUR) composite coating. The lowest inhibitory concentration of CTS/CUR composite coating on Serratia marcescens and Pseudomonas syringae, the growth curves, and the changes of the cell lysis rate were determined to explore the inhibitory mechanism of CTS/CUR composite coating on Serratia marcescens and Pseudomonas syringae and the microscopic morphology of Serratia marcescens and Pseudomonas syringae was observed using scanning electron microscopy at the same time. The results showed that the CTS/CUR composite coating could effectively inhibit the growth of Serratia marcescens and Pseudomonas, and the inhibitory effect reflected the concentration-dependent characteristics. The electron microscopy results indicated that the inhibition of Serratia marcescens and Pseudomonas syringae by the CTS/CUR composite coating might originate from its disruptive effect on the cell wall and cell membrane of the bacterium.

Distinct Denitrifying Phenotypes of Predominant Bacteria Modulate Nitrous Oxide Metabolism in Two Typical Cropland Soils

Denitrifying nitrous oxide (N₂O) emissions in agroecosystems result from variations in microbial composition and soil properties. However, the microbial mechanisms of differential N₂O emissions in agricultural soils are less understood. In this study, microcosm experiments using two main types of Chinese cropland soil were conducted with different supplements of nitrate and glucose to simulate the varying nitrogen and carbon conditions. The results show that N₂O accumulation in black soil (BF) was significantly higher than that in fluvo-aquic soil (FF) independent of nitrogen and carbon. The abundance of most denitrifying genes was significantly higher in FF, but the ratios of genes responsible for N₂O production (nirS and nirK) to the gene responsible for N₂O reduction (nosZ) did not significantly differ between the two soils. However, the soils showed obvious discrepancies in denitrifying bacterial communities, with a higher abundance of N₂O-generating bacteria in BF and a higher abundance of N₂O-reducing bacteria in FF. High accumulation of N₂O was verified by the bacterial isolates of Rhodanobacter predominated in BF due to a lack of N₂O reduction capacity. The dominance of Castellaniella and others in FF led to a rapid reduction in N₂O and thus less N₂O accumulation, as demonstrated when the corresponding isolate was inoculated into the studied soils. Therefore, the different phenotypes of N₂O metabolism of the distinct denitrifiers predominantly colonized the two soils, causing differing N₂O accumulation. This knowledge would help to develop a strategy for mitigating N₂O emissions in agricultural soils by regulating the phenotypes of N₂O metabolism.

Potential of a novel facultative anaerobic denitrifying Cupriavidus sp. W12 to remove fluoride and calcium through calcium bioprecipitation

This study focused on a novel denitrifying Cupriavidus sp. W12, which can perform microbial induced calcium precipitation (MICP) to remove fluoride (F^-) under aerobic and anaerobic conditions. Under anaerobic condition, the removal ratios of F^-, calcium (Ca²⁺), and nitrate (NO₃^--N) reached 87.52%, 65.03%, and 96.06%, respectively, which were higher than that under aerobic condition (50.17%, 88.21%, and 67.33%, respectively). Higher pH of 8.26 was obtained after 120 h of the strain W12 growth under anaerobic condition than that under aerobic condition (7.77). The F^- removal ratio of 98.20% was predicted by the response surface methodology (RSM). Scanning electron microscopy (SEM) images of anaerobic precipitation were dense and porous. CaCO₃, Ca₅(PO₄)₃OH, Ca₅(PO₄)₃F, and CaF₂ were determined by X-ray diffraction (XRD) and energy dispersive spectrometer (EDS). Self-aggregation of bacteria and adsorption of biological crystal seeds were the determinant of the precipitates formation. The results of infrared spectrometer (FTIR) and excitation-emission matrix (EEM) showed that anaerobic extracellular polymeric substances (EPS) expression led the proportion of hydroxylapatite in the precipitates increased. As the first report on the anaerobic MICP to remove F^-, it provides a theoretical basis for the remediation of F^-, Ca²⁺, and NO₃^--N in groundwater.

Cross-Feeding between Members of Thauera spp. and Rhodococcus spp. Drives Quinoline-Denitrifying Degradation in a Hypoxic Bioreactor

We experimentally verified that the second most abundant taxon, Rhodococcus, played a role in degrading quinoline to 2-hydroxyquinoline, while the most abundant taxon, Thauera, degraded 2-hydroxyquinoline. Metabolites from Thauera further served to provide metabolites for Rhodococcus. Hence, an ecological guild composed of two isolates was assembled, revealing the different roles that keystone organisms play in the microbial community. This report, to the best of our knowledge, is the first on cross-feeding between the initial quinoline degrader and a second bacterium. Specifically, the quinoline degrader (Rhodococcus) did not benefit metabolically from quinoline degradation to 2-hydroxyquinoline but instead benefited from the metabolites produced by the second bacterium (Thauera) when Thauera degraded the 2-hydroxyquinoline. These results could be a significant step forward in the elucidation of the microbial mechanism underlying quinoline-denitrifying degradation.

The complex bacterial community in a quinoline-degrading denitrifying bioreactor is predominated by several taxa, such as Thauera and Rhodococcus. However, it remains unclear how the interactions between the different bacteria mediate quinoline metabolism under denitrifying conditions. In this study, we designed a sequence-specific amplification strategy to isolate the most predominant bacteria and obtained four strains of Thauera aminoaromatica, a representative of a key member in the bioreactor. Tests on these isolates demonstrated that all were unable to degrade quinoline but efficiently degraded 2-hydroxyquinoline, the hypothesized primary intermediate of quinoline catabolism, under nitrate-reducing conditions. However, another isolate, Rhodococcus sp. YF3, corresponding to the second most abundant taxon in the same bioreactor, was found to degrade quinoline via 2-hydroxyquinoline. The end products and removal rate of quinoline by isolate YF3 largely varied according to the quantity of available oxygen. Specifically, quinoline could be converted only to 2-hydroxyquinoline without further transformation under insufficient oxygen conditions, e.g., less than 0.5% initial oxygen in the vials. However, resting YF3 cells aerobically precultured in medium with quinoline could anaerobically convert quinoline to 2-hydroxyquinoline. A two-strain consortium constructed with isolates from Thauera (R2) and Rhodococcus (YF3) demonstrated efficient denitrifying degradation of quinoline. Thus, we experimentally verified that the metabolic interaction based on 2-hydroxyquinoline cross-feeding between two predominant bacteria constitutes the main quinoline degradation mechanism. This work uncovers the mechanism of quinoline removal by two cooperative bacterial species existing in denitrifying bioreactors.

IMPORTANCE We experimentally verified that the second most abundant taxon, Rhodococcus, played a role in degrading quinoline to 2-hydroxyquinoline, while the most abundant taxon, Thauera, degraded 2-hydroxyquinoline. Metabolites from Thauera further served to provide metabolites for Rhodococcus. Hence, an ecological guild composed of two isolates was assembled, revealing the different roles that keystone organisms play in the microbial community. This report, to the best of our knowledge, is the first on cross-feeding between the initial quinoline degrader and a second bacterium. Specifically, the quinoline degrader (Rhodococcus) did not benefit metabolically from quinoline degradation to 2-hydroxyquinoline but instead benefited from the metabolites produced by the second bacterium (Thauera) when Thauera degraded the 2-hydroxyquinoline. These results could be a significant step forward in the elucidation of the microbial mechanism underlying quinoline-denitrifying degradation.

Spreading of extended-spectrum β-lactamase-producing Escherichia coli ST131 and Klebsiella pneumoniae ST11 in patients with pneumonia: a molecular epidemiological study

Supplemental Digital Content is available in the text

Background:

Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae) are the important pathogens causing pneumonia. This study aimed to investigate the clinical characteristics and molecular epidemiology of ESBL-producing E. coli and K. pneumoniae causing pneumonia at a large teaching hospital in China.

Methods:

We collected patient's clinical data and ESBL-producing E. coli and K. pneumoniae strains causing pneumonia (from December 2015 to June 2016) at a hospital in Wuhan. The susceptibilities, multi-locus sequence typing, homologous analysis, ESBL genes by polymerase chain reaction and sequencing were determined.

Results:

A total of 59 ESBL-producing strains (31 E. coli and 28 K. pneumoniae) isolated from patients with pneumonia were analyzed. The majority of strains were isolated from patients were with hospital-acquired pneumonia (37/59, 62.7%), followed by community-acquired pneumonia (13/59, 22.0%), and ventilator-related pneumonia (9/59, 15.3%). The E. coli ST131 (9 isolates, 29.0%) and K. pneumoniae ST11 (5 isolates, 17.9%) were the predominant sub-types. The most prevalent ESBL gene was CTX-M-14, followed by SHV-77, CTX-M-3, SHV-11, and CTX-M-27. At least 33 (55.9%) of the ESBL-producing strains carried two or more ESBL genes. The ISEcp1 and IS26 were found upstream of all blaCTX-M (CTX-Ms) and of most blaSHV (SHVs) (57.6%), respectively. Moreover, three ESBL-producing K. pneumoniae ST11 strains which were resistant to carbapenems carried the bla_NDM-1 and bla_KPC-2, two of which also bearing bla_OXA-48 were resistant to all antibiotics (including Tigecycline).

Conclusions:

Hospital-acquired pneumonia is more likely correlated with ESBL-producing E. coli and K. pneumoniae. ESBL-producing E. coli ST131 and multi-drug resistance ESBL-producing, as well as New Delhi metallo-β-lactamase-1 (NDM-1) and Klebsiella pneumoniae carbapenemases-2 (KPC-2) bearing K. pneumoniae ST11 are spreading in patients with pneumonia in hospital.

Screening and Diversity Analysis of Aerobic Denitrifying Phosphate Accumulating Bacteria Cultivated from A2O Activated Sludge

The aerobic denitrifying phosphate accumulating bacteria (ADPB) use NO3− as an electron acceptor and remove nitrate by denitrification and concomitant uptake of excessive phosphorus in aerobic conditions. Activated sludge was collected from the A2O aerobic biological pool of the sewage treatment plant at Hezuo Town, Chengdu City. The candidate ADPB strains were obtained by cultivation in the enriched denitrification media, followed by repeated isolation and purification on bromothymol blue (BTB) solid plates. The obtained candidates were further screened for ADPB strains by phosphorus uptake experiment, nitrate reduction test, metachromatic granules staining, and poly-β-hydroxybutyrate (PHB) staining. The 16 sedimentation ribosome deoxyribonucleic acid (16 S rDNA) molecular technique was used to determine their taxonomy. Further, the denitrification and dephosphorization capacities of ADPB strains were ascertained through their growth characteristics in nitrogen-phosphorus-rich liquid media. The results revealed a total of 25 ADPB strains screened from the activated sludge of the A2O aerobic biological pool of the sewage treatment plant at Hezuo Town. These strains belonged to two classes, four orders, and five genera. Among them, the strain SW18NP2 was a potentially new species in the Acinetobacter genus, while the strain SW18NP24 was a potential new species in the Pseudomonas genus at the time of their characterization. The Acinetobacter was the dominant genus. The obtained ADPB strains demonstrated a rich diversity. The ADPB strains had significant variations in denitrification and dephosphorization capacities. Twenty-three strains exhibited a total phosphorus removal rate of above 50%, and 19 strains exhibited a total nitrogen removal rate of above 50%. The strain SW18NP2 showed the best denitrifying phosphorus removal (DPR) capacity, with a dephosphorization rate of 82.32% and a denitrification rate of 73.73%. The ADPB in the A2O aerobic biological pool of the sewage treatment plant at Hezuo Town demonstrated a rich diversity and a strong DPR capacity.

Characteristics of Inorganic Phosphate-Solubilizing Bacteria from the Sediments of a Eutrophic Lake

Inorganic phosphate-solubilizing bacteria (IPB) are an important component of microbial populations in lake sediments. The phosphate that they decompose and release becomes an important source of phosphorus for eutrophic algae. The IPB strains were screened and isolated from the sediments of Sancha Lake using National Botanical Research Institute’s phosphate (NBRIP) plates. Their taxonomy was further determined by the 16S rDNA technique. The tricalcium phosphate-solubilizing ability of obtained IPB strains was evaluated using NBRIP- bromophenol blue (BPB) plates and Pikovskaya (PVK) liquid medium. Then, the ability of IPB strains to release phosphorus from the sediments were investigated by mimicking the lake environment. In this study, a total of 43 IPB strains were screened and isolated from the sediments of Sancha Lake, belonging to three phyla, eight families, and ten genera. Among them, two potentially new strains, SWSI1728 and SWSI1734, belonged to genus Bacillus, and a potentially new strain, SWSI1719, belonged to family Micromonosporaceae. Overall, the IBP strains were highly diverse and Bacillus and Paenibacillus were the dominant genera. In the tricalcium phosphate-solubilizing experiment, only 30 of the 43 IPB strains exhibited clear halo zones on plates, while in the liquid culture experiment, all strains were able to dissolve tricalcium phosphate. The phosphate-solubilizing abilities of the strains varied significantly, and the strain SWSI1725 of the Bacillus genus showed the strongest ability with a phosphate-solubilizing content of 103.57 mg/L. The sterilized systems demonstrated significantly elevated phosphorus hydrochloride (HCl–P) decomposition and release from the sediments after the inoculation of IPB strains, whereas no significant effect was demonstrated on the phosphonium hydroxide (NaOH-P). Thus, the IPB strains in the sediments of Sancha Lake possessed rich diversity and the ability to release phosphorus in sediments.

Antidepressant-Like Effects of Cistanche tubulosa Extract on Chronic Unpredictable Stress Rats Through Restoration of Gut Microbiota Homeostasis

Growing evidence shows that neuropsychiatric disorders, such as depression, are linked with gut microbiome through the gut–brain axis. Cistanches Herba is well known for the treatment of “kidney-yang” deficiency in traditional Chinese medicine (TCM), and has been used for treatment of neurodegenerative diseases in recent years. In this study, chronic unpredictable stress (CUS)-induced depression model was established to explore the impact of Cistanche tubulosa extract (CTE) on behavioral tests, monoamine neurotransmitters and neurotrophic factors in hippocampus and colon, gut microbiota composition, and short-chain fatty acids (SCFAs) production. Moreover, correlation analysis was used to evaluate the functional relationship between altered gut microbiota, changed neurotransmitters and neurotrophins in hippocampus and colon, and disturbed concentration of SCFAs. CTE significantly improved depression-like behaviors in rats under CUS. Brain level of 5-hydroxytryptamine (5-HT) and brain-derived neurotrophic factor (BDNF) expression in CUS rats were restored by CTE. The relative abundance of gut microbiota and the concentrations of acetate and hexanoic acid could also be modulated by CTE treatment. We further showed that the application of CTE in CUS rats led to strong correlation among disrupted gut microbiota composition, hippocampus neurotransmitter levels, and production of neuroactive metabolite SCFAs. Altogether, these results identify CTE as a potential treatment for depressive symptoms by restoring homeostasis of gut microbiota for microbiota–gut–brain axis disorders, opening new avenues in the field of neuropsychopharmacology.

Mosapride Stabilizes Intestinal Microbiota to Reduce Bacterial Translocation and Endotoxemia in CCl4-Induced Cirrhotic Rats

BACKGROUND

Impaired intestinal motility may lead to the disruption of gut microbiota equilibrium, which in turn facilitates bacterial translocation (BT) and endotoxemia in cirrhosis. We evaluated the influence of mosapride, a prokinetic agent, on BT and DNA fingerprints of gut microbiota in cirrhotic rats.

METHODS

A rat model of cirrhosis was set up via subcutaneous injection of carbon tetrachloride (CCl₄). The portal pressure, liver and intestinal damage, plasma endotoxin, BT, and intestinal transit rate (ITR) of cirrhotic rats were determined. Fecal DNA fingerprints were obtained by ERIC-PCR. The expressions of tight junction proteins were evaluated by western blotting.

RESULTS

Mosapride treatment to cirrhotic rats significantly reduced the plasma endotoxin level and incidence of BT, accompanied by increased ITR. Cirrhotic rats (including those treated with mosapride) suffered from BT exhibited significantly lower ITR than those who are free of BT. Pearson coefficient indicated a significant and negative correlation between the plasma endotoxin level and ITR. The genomic fingerprints of intestinal microbiota from the three groups fell into three distinctive clusters. In the mosapride-treated group, Shannon's index was remarkably increased compared to the model group. Significantly positive correlation was detected between Shannon's index and ITR. Mosapride did not improve hepatic and intestinal damages and ileal expressions of occludin and ZO-1.

CONCLUSIONS

Mosapride significantly increases intestinal motility in cirrhotic rats, thus to recover the disordered intestinal microbiota, finally resulting in decreased plasma endotoxin and BT.

Development of Human Breast Milk Microbiota-Associated Mice as a Method to Identify Breast Milk Bacteria Capable of Colonizing Gut

Human breast milk is recognized as one of multiple important sources of commensal bacteria for infant gut. Previous studies searched for the bacterial strains shared between breast milk and infant feces by isolating bacteria and performing strain-level bacterial genotyping, but only limited number of milk bacteria were identified to colonize infant gut, including bacteria from Bifidobacterium, Staphylococcus, Lactobacillus, and Escherichia/Shigella. Here, to identify the breast milk bacteria capable of colonizing gut without the interference of bacteria of origins other than the milk or the necessity to analyze infant feces, normal chow-fed germ-free mice were orally inoculated with the breast milk collected from a mother 2 days after vaginal delivery. According to 16S rRNA gene-based denaturant gradient gel electrophoresis and Illumina sequencing, bacteria at >1% abundance in the milk inoculum were only Streptococcus (56.0%) and Staphylococcus (37.4%), but in the feces of recipient mice were Streptococcus (80.3 ± 2.3%), Corynebacterium (10.0 ± 2.6 %), Staphylococcus (7.6 ± 1.6%), and Propionibacterium (2.1 ± 0.5%) that were previously shown as dominant bacterial genera in the meconium of C-section-delivered human babies; the abundance of anaerobic gut-associated bacteria, Faecalibacterium, Prevotella, Roseburia, Ruminococcus, and Bacteroides, was 0.01–1% in the milk inoculum and 0.003–0.01% in mouse feces; the abundance of Bifidobacterium spp. was below the detection limit of Illumina sequencing in the milk but at 0.003–0.01% in mouse feces. The human breast milk microbiota-associated mouse model may be used to identify additional breast milk bacteria that potentially colonize infant gut.

Effect of competitive exclusion in rabbits using an autochthonous probiotic

<p>Animal nutrition has been severely challenged by the ban on antimicrobials as growth promoters. This has fostered the study of alternative methods to avoid colonisation by pathogenic bacteria as well as to improve the growth of animals and feed conversion efficiency. These new options should not alter the normal intestinal microbiota, or affect it as little as possible. The use of probiotics, which are live microorganisms that beneficially affect the host by improving its intestinal microbial balance, can be seen as a promising way to achieve that goal. In this study, New Zealand White rabbits were fed diets containing an autochthonous probiotic of Enterococcus spp., with the strains EaI, EfaI and EfaD, and Escherichia coli, with the strains ECI 1, ECI 2 and ECD, during a 25-d trial, to evaluate the impact of the probiotic on the faecal microbiota, including population dynamics and antimicrobial resistance profiles. A control group of rabbits, which was fed a diet containing a commonly used mixture of antimicrobials (colistin, oxytetracycline, and valnemulin), was also studied. To assess the colonisation ability of the mentioned probiotic, the faecal microbiota of the rabbits was characterised up to 10 d after the administration had ended. Isolates of enterococci and E. coli were studied for phylogenetic relationships using enterobacterial repetitive intergenic consensus (ERIC-PCR) and pulse-field gel electrophoresis (PFGE), respectively. Although partially affected by an unexpected clinical impairment suffered by the rabbits in the experimental group, our results showed the following. The difference between the growth rate of the animals treated with antimicrobials and those fed the probiotic was not statistically significant (P&gt; 0.05). The competitive exclusion product was present in the faecal samples in a large proportion, but stopped being recovered by culture as soon as the administration ended and the housing conditions were changed. Multidrug-resistant strains of enterococci and E. coli were more commonly recovered from faecal samples of animals fed diets containing antimicrobials, than from rabbits fed diets with our probiotic formula. The use of E. coli probiotics to prevent infection by enteropathogenic strains must be carefully considered due to the possible occurrence of gastrointestinal signs. On the other hand, enterococci strains may be more effective, but lack the long-term colonisation ability.</p>

Characterisation of Commensal Escherichia coli Isolated from Apparently Healthy Cattle and Their Attendants in Tanzania

While pathogenic types of Escherichia coli are well characterized, relatively little is known about the commensal E. coli flora. In the current study, antimicrobial resistance in commensal E. coli and distribution of ERIC-PCR genotypes among isolates of such bacteria from cattle and cattle attendants on cattle farms in Tanzania were investigated. Seventeen E. coli genomes representing different ERIC-PCR types of commensal E. coli were sequenced in order to determine their possible importance as a reservoir for both antimicrobial resistance genes and virulence factors. Both human and cattle isolates were highly resistant to tetracycline (40.8% and 33.1%), sulphamethazole-trimethoprim (49.0% and 8.8%) and ampicillin (44.9% and 21.3%). However, higher proportion of resistant E. coli and higher frequency of resistance to more than two antimicrobials was found in isolates from cattle attendants than isolates from cattle. Sixteen out of 66 ERIC-PCR genotypes were shared between the two hosts, and among these ones, seven types contained isolates from cattle and cattle attendants from the same farm, suggesting transfer of strains between hosts. Genome-wide analysis showed that the majority of the sequenced cattle isolates were assigned to phylogroups B1, while human isolates represented phylogroups A, C, D and E. In general, in silico resistome and virulence factor identification did not reveal differences between hosts or phylogroups, except for lpfA and iss found to be cattle and B1 phylogroup specific. The most frequent plasmids replicon genes found in strains from both hosts were of IncF type, which are commonly associated with carriage of antimicrobial and virulence genes. Commensal E. coli from cattle and attendants were found to share same genotypes and to carry antimicrobial resistance and virulence genes associated with both intra and extraintestinal E. coli pathotypes.

Protective effect of polysaccharides fractions from Sijunzi decoction in reserpine-induced spleen deficiency rats

Polysaccharide fraction S-3 from SJZD could mitigate effect in the reserpine-induced rats which was investigated with a comprehensive screening strategy.

Effects of broad-spectrum antibiotics on the metabolism and pharmacokinetics of ginsenoside Rb1: a study on rats׳ gut microflora influenced by lincomycin

Ginsenoside Rb1 is a biologically active compound that is abundant in ginseng (Panax ginseng). It has been reported that ginsenosides could be metabolized by enzymes and bacteria in the large intestine. In this study, the effects of intestinal bacteria on the metabolism and pharmacokinetics of ginsenoside Rb1 were investigated using lincomycin-treated rat models (4.8g/kg and 0.12g/kg). Specifically, ginsenoside Rb1 was incubated anaerobically with rat fecal suspensions obtained from the control and two model groups at 0, 6, 12, 24, and 48h. Ginsenoside Rb1 and its metabolites were determined by HPLC analysis. Compared with the normal rats case where Rd and compound K were detected in the incubation mixture, ginsenoside Rd and F2 were found in the 0.12g/kg group, but only Rd was found in the 4.8g/kg group. Moreover, fecal β-glucosidase activity was significantly lower in lincomycin-treated (0.12g/kg and 4.8g/kg) model rats. After administration of Rb1 to rats, ginsenoside Rb1 and its metabolites Rd, Rg3, and Rh2 were detectable in normal rat urine, whereas none was detected in the two model groups. The plasma concentration-time Rb1 were compared between model groups and normal rats. The systemic exposure as evidenced by the AUC and T1/2 values was significantly higher in model groups than in normal rats. Our findings demonstrated that consumption of lincomycin could lead to the formation of specific metabolites and pharmacokinetic changes of ginsenoside Rb1 in the gut, attributed to alterations in metabolic activities of intestinal bacteria. Our results also suggested that patients who want to use intestinal bacteria-metabolized drugs such as ginseng (Panax ginseng) should pay attention to the profile of intestinal bacteria or potential drug interactions to ensure therapeutic efficacy.

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.

The bacterial amyloid curli is associated with urinary source bloodstream infection

Urinary tract infections are the most common cause of E. coli bloodstream infections (BSI) but the mechanism of bloodstream invasion is poorly understood. Some clinical isolates have been observed to shield themselves with extracellular amyloid fibers called curli at physiologic temperature. We hypothesize that curli fiber assembly at 37°C promotes bacteremic progression by urinary E. coli strains. Curli expression by cultured E. coli isolates from bacteriuric patients in the presence and absence of bacteremia were compared using Western blotting following amyloid fiber disruption with hexafluoroisopropanol. At 37°C, urinary isolates from bacteremic patients were more likely to express curli than those from non-bacteremic patients [16/22 (73%) vs. 7/21 (33%); p = 0.01]. No significant difference in curli expression was observed at 30°C [86% (19/22) vs. 76% (16/21); p = 0.5]. Isolates were clonally diverse between patients, indicating that this phenotype is distributed across multiple lineages. Most same-patient urine and blood isolates were highly related, consistent with direct invasion of urinary bacteria into the bloodstream. 37°C curli expression was associated with bacteremic progression of urinary E. coli isolates in this population. These findings suggest new future diagnostic and virulence-targeting therapeutic approaches.

Evaluation of the Biofilm-Forming Ability and Genetic Typing for Clinical Isolates ofPseudomonas aeruginosaby Enterobacterial Repetitive Intergenic Consensus-Based PCR

Biofilm formation is an important phenotype associated with chronic Pseudomonas aeruginosa infections. In the present study, a total of 48 P. aeruginosa strains isolated from clinical specimens were examined for their biofilm-forming ability using a microtiter plate method. The different biofilm-forming abilities were demonstrated among the strains; however, most strains formed a larger biofilm than strain PAO1, a reference strain. The genetic typing was also carried out by enterobacterial repetitive intergenic consensus-based polymerase chain reaction. Although they were divided into five groups (A to E), most of the strains showing the higher biofilm-forming ability were found to be in groups D and E, suggesting a significant relationship between the biofilm-forming ability and the genetic group.

Evaluation of the intestinal microbial diversity in miniature pig after orally infected with Entamoeba histolytica

The objective of this study was to analyze the difference in intestinal microbial diversity between healthy and (Entamoeba histolytica) orally infected minipig. Enterobacterial repetitive intergenic consensus (ERIC)-PCR was applied to analyze this diversity and dynamic change, including the duodenum, jejunum, ileum, cecum, and rectum from healthy and orally infected minipig at different time points. The results showed that the intestinal microbial community of the control minipigs was stable and the ERIC-PCR band numbers of the control minipigs were the lowest in the rectum and highest in the cecum. ERIC-PCR bands of orally inoculated minipigs showed no obvious change until 24 h after postinoculation (hpi). The numbers of the ERIC-PCR bands gradually decreased from 24 to 72 hpi, then, with the development of disease, the band numbers gradually increased until 6 days postinoculation. The prominent bacteria had changed in the presence of E. histolytica infection and the DNAstar of staple of ERIC-PCR showed that obligate aerobes and facultative aerobes (Escherichia coli, Shigella, Salmonella) became the preponderant bacilli in the intestine of orally infected minipigs with E. histolytica. This study has provided significant data to clarify the intestinal microbial diversity and dynamic change of healthy and E. histolytica orally infected minipigs.

Intestinal microbial community diversity between healthy and orally infected rabbit with Entamoeba histolytica by ERIC-PCR

Enterobacterial repetitive intergenic consensus (ERIC)-PCR was applied to analyze the difference of intestinal microbial community diversity between healthy and orally infected rabbits with Entamoeba histolytica. The dynamic changes in different parts of digestive system including the duodenum, jejunum, ileum, caecum, and rectum in healthy and infected rabbits at different time points were also tested. The intestinal microbial community of the control healthy rabbits was steady, and the total number of ERIC-PCR bands in the control healthy rabbit was the least in the rectum and the most in the caecum. ERIC-PCR bands of orally inoculated rabbits did not obviously change until 24 h after postinoculation (p.i.). The numbers of the ERIC-PCR bands gradually decreased from 24 to 72 h p.i., and then, with the development of disease, the band numbers gradually increased until 6 days p.i. Sequence analysis showed that the nucleotide sequence homologies of the fragment about 1,200 bp of infected ileum sampled at 32 h p.i. were above 95 % with Sinorhizobium meliloti enterobacterial, Erwinia amylovora and Salmonella typhimurium, and the nucleotide sequence homologies of the fragment about 300 bp of infected ileum sampled at 48 h p.i. were more than 90 % with Xanthomonas campestris enterobacterial, Yersinia enterocolitica subsp., Shigella flexneri, S. meliloti enterobacterial, Yersinia pestis, Klebsiella pneumoniae subsp., and Escherichia coli. The prominent bacteria had changed after E. histolytica infection. The DNAstar of staple of ERIC-PCR showed that aerobe and facultative aerobe (E. coli, Shigella, and Salmonella) became preponderant bacilli in the intestine of orally infected rabbits with E. histolytica.

Cadmium and mercury removal from non-point source wastewater by a hybrid bioreactor

The purpose of this study was to remove cadmium (Cd) and mercury (Hg) from non-point source wastewater by a hybrid bioreactor consisting of two different processes (anaerobic-anoxic-aerobic and photoautotrophic). The results showed that the bioreactor could concurrently culture heterotrophic and autotrophic microorganisms, and removed Cd and Hg from the wastewater successfully. The average removal efficiencies were 79% and 66%, respectively for Cd and Hg. The relationship between Cd removal rate and biofilm mass was observed to be significant (p<0.05) during different seasons. The Hg removal was mainly due to the bioaccumulation in macrophytes via a photoautotrophic process. Due to the increase of the bacterial diversity under the rejuvenated conditions modulated by the hybrid bioreactor, the growth conditions of the native bacterial habitat were improved. The results demonstrate that the environmentally benign, easily-deployed, sludge free and cost-effective hybrid bioreactor can efficiently remove Cd and Hg from non-point source wastewater.

The removal of nutrients from non-point source wastewater by a hybrid bioreactor

The aim of this project was to establish an economical and environmentally benign biotechnology for removing nutrients from non-point source wastewater. The proposal involves a hybrid bioreactor comprised of sequential anaerobic, anoxic and aerobic (A(2)/O) processes and an eco-ditch being constructed and applied in a suburban area, Kunming, south-western China, where wastewater was discharged from an industrial park and suburban communities. The results show that the hybrid bioreactor fosters heterotrophic and autotrophic microorganisms. When the hydraulic load is 200 m(3) per day with the running mode in 12h cycles, the removal efficiencies of the nutrients were 81% for TP, 74% for TDP, 82% for TN, 79% for NO(3)-N and 86% for NH(4)-N. The improved bacterial community structure and bacterial habitats further implied enhanced water quality and indicates that the easily-deployed, affordable and environmentally-friendly hybrid bioreactor is a promising bio-measure for removing high loadings of nutrients from non-point source wastewater.

Intraspecies discrimination of Lactobacillus paraplantarum by PCR

Lactobacillus paraplantarum is a species phenotypically close to Lactobacillus plantarum. Several PCR methods were evaluated to discriminate L. paraplantarum strains and among them, a PCR using an enterobacterial repetitive intergenic consensus (ERIC) sequence differentiated L. paraplantarum from other Lactobacillus species. In addition, a combination of ERIC and random amplified polymorphic DNA (RAPD) analysis distinguished among seven strains of L. paraplantarum tested. ERIC-PCR profiles showed several strain-specific DNA fragments in L. paraplantarum, among them, a 2.2-kb ERIC marker, termed LpF1, found to be specific to strain FBA1, which improved the skin integrity in an animal model. The LpF1 encodes three proteins similar to Lactobacillus fermentum AroA, TyrA, and AroK, which are involved in the shikimate pathway. A primer pair specific to FBA1 based on the internal sequence of LpF1 amplified a 950-bp FBA1-specific fragment LpF2. Southern blot analysis of Dra I-digested genomic DNA of L. paraplantarum strains using LpF2 as a probe showed that LpF2 is distinctive of strain FBA1 among 16 L. paraplantarum strains. Because both ERIC- and RAPD-PCR are fast and technically simple methods, they are useful for the rapid discrimination of L. paraplantarum strains and for the development of new strain-specific DNA markers for identifying industrially important strains.

A multi-level bioreactor to remove organic matter and metals, together with its associated bacterial diversity

The purpose of this study was to treat complex wastewater consisting of domestic wastewater, tobacco processing and building materials washings. The proposed multi-level bioreactor consists of a biopond-biofilter, anoxic/aerobic (A/O) fluidized beds and a photoautotrophic system. The results show that when the hydraulic load of the bioreactor was 200 m3/d, it successfully and simultaneously removed the organic matter and metals. When the bioreactor was in a relatively steady-state condition, the overall average organic matter and metals removal efficiencies are as follows, COD (89%), UV245 nm-matter (91%), Cu (78%), Zn (79%) and Fe (84%). The growth conditions of the native bacterial habitat were improved, which resulted from the increase of the in bacterial diversity under the rejuvenated conditions induced by the bioreactor. The results demonstrate that the multi-level bioreactor, without a sludge treatment system, can remove heterogeneous organic matter and metals from wastewater.

Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice

Both genetic variations and diet-disrupted gut microbiota can predispose animals to metabolic syndromes (MS). This study assessed the relative contributions of host genetics and diet in shaping the gut microbiota and modulating MS-relevant phenotypes in mice. Together with its wild-type (Wt) counterpart, the Apoa-I knockout mouse, which has impaired glucose tolerance (IGT) and increased body fat, was fed a high-fat diet (HFD) or normal chow (NC) diet for 25 weeks. DNA fingerprinting and bar-coded pyrosequencing of 16S rRNA genes were used to profile gut microbiota structures and to identify the key population changes relevant to MS development by Partial Least Square Discriminate Analysis. Diet changes explained 57% of the total structural variation in gut microbiota, whereas genetic mutation accounted for no more than 12%. All three groups with IGT had significantly different gut microbiota relative to healthy Wt/NC-fed animals. In all, 65 species-level phylotypes were identified as key members with differential responses to changes in diet, genotype and MS phenotype. Most notably, gut barrier-protecting Bifidobacterium spp. were nearly absent in all animals on HFD, regardless of genotype. Sulphate-reducing, endotoxin-producing bacteria of the family, Desulfovibrionaceae, were enhanced in all animals with IGT, most significantly in the Wt/HFD group, which had the highest calorie intake and the most serious MS phenotypes. Thus, diet has a dominating role in shaping gut microbiota and changes of some key populations may transform the gut microbiota of Wt animals into a pathogen-like entity relevant to development of MS, despite a complete host genome.

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.

Intestinal microflora molecular markers of spleen-deficient rats and evaluation of traditional Chinese drugs

AIM: To find a rapid and efficient analysis method of gastrointestinal microflora in Pi-deficient (spleen-deficient) rats and to evaluate traditional Chinese drugs.

METHODS: Enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) based assay was performed to examine changes of intestinal microflora in two Pi-deficienct animal models and to evaluate the efficacy of four traditional Chinese drugs as well as a probiotic recipe and another therapy in Pi-deficient rats.

RESULTS: A molecular marker was identified for Pi-deficiency in rats. The pharmacodynamic evaluation system, including identified molecular markers (net integral area and abundance of DNA bands), Shannon’s index for diversity of intestinal microflora, and Sorenson’s pairwise similarity coefficient, was established. The four major clinical recipes of traditional Chinese drugs for Pi-deficiency in rats, especially at their medium dose (equivalence to the clinical dose), produced more pronounced recovery activities in Pi-deficient rats, while higher doses of these recipes did not show a better therapeutic effect but some toxic effects such as perturbation deterioration of intestinal microflora.

CONCLUSION: Both fingerprint analysis and identified marker can show Pi-deficiency in rats and its difference after treatment. The identified molecular marker may be applied in screening for the active compounds both in relative traditional Chinese drugs and in pharmacodynamic study of Pi-deficiency in rats.

New strategies for electrophoresis analysis of enterobacterial repetitive intergenic consensus PCR in animal intestinal microflora

Enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) is a molecular biological technology that can be used to study microbial community diversity and dynamics. In many reports, investigations of microbial diversity from environmental samples were based on the agarose gel electrophoresis (AGE) patterns of ERIC-PCR amplified products. This is not a sound practice, since bands with identical positions can contain different sequences; thus, this practice could possibly exaggerate the similarities or diversities among samples. To mitigate this issue, we employed a denaturing gradient gel electrophoresis (DGGE) strategy to explore DNA bands with the same size, between ERIC-PCR profiles of samples. DPS software was used with Shannon-Wiener diversity index (H') to analyze ERIC-PCR fingerprint profiles. H' revealed that the microbial community diversity at DGGE was higher than with AGE. The results of this study suggest that the ERIC-PCR assays with DGGE can provide a better assessment of electrophoresis pattern with regards to the structure of an intestinal microbial community.

Fatal infection in human flora-associated piglets caused by the opportunistic pathogen Klebsiella pneumoniae from an apparently healthy human donor

Seventeen out of 24 human flora-associated (HFA) piglets died after oral administration of whole fecal flora from an apparently healthy human donor. The bacteria isolated from the organs of the infected piglets were identified as Klebsiella pneumoniae by bacteriological and biochemical tests and 16S rRNA gene sequence analysis. The identical K. pneumoniae strain was also isolated from the donor's fecal flora. All three neonatal piglets inoculated with K. pneumoniae from the donor's fecal flora developed severe diarrhea, with 2 eventually dying. This strongly suggests that the opportunistic pathogen K. pneumoniae from the human donor caused the fatal infection in the HFA piglets. The results underscore the importance of safety evaluation of the human donor's fecal flora for HFA piglet development.

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.

Comparative analysis of intestinal microbial community diversity between healthy and orally infected ducklings with Salmonella enteritidis by ERIC-PCR

AIM: To analyze the difference of intestinal microbial community diversity between healthy and (S. enteritidis) orally infected ducklings.

METHODS: Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR was applied to analyze the intestinal microbial community diversity and dynamic change including duodenum, jejunum, ileum, cecum and rectum from healthy ducklings and 7-day-old ducklings after oral infection with S. enteritidis at different time points.

RESULTS: The intestinal microbial community of the control healthy ducklings was steady and the ERIC-PCR band numbers of the control healthy ducklings were the least with rectum and were the most with caecum. ERIC-PCR bands of orally inoculated ducklings did not obviously change until 24 h after inoculation (p.i.). The numbers of the ERIC-PCR bands gradually decreased from 24 h to 72 h p.i., and then, with the development of disease, the band numbers gradually increased until 6 d p.i. The prominent bacteria changed because of S. enteritidis infection and the DNAstar of staple of ERIC-PCR showed that aerobe and facultative aerobe (Escherichia coli, Shigella, Salmonella) became preponderant bacilli in the intestine of orally infected ducklings with SE.

CONCLUSION: This study has provided significant data to clarify the intestinal microbial community diversity and dynamic change of healthy and S. enteritidis orally infected ducklings, and valuable insight into the pathogenesis of S. enteritidis infection in both human and animals.

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.

Cloning of environmental genomic fragments as physical markers for monitoring microbial populations in coking wastewater treatment system

The association between community functional shift and dynamics of genomic DNA composition can be used to identify functionally relevant populations as indicator organisms for systems monitoring. In this work, fingerprinting-based community DNA hybridization was used to monitor community structural dynamics and identify genomic fragments whose abundance shifts were concomitant to changes in COD removal capacity in a reactor. A laboratory-scale anaerobic-anoxic-oxic fixed biofilm system treating coking wastewater was operated with (LR mode) or without effluent recirculation (LNR mode). The contribution to total chemical oxygen demand (COD) removal by the anoxic reactor increased from 4% in LNR mode to 26% in LR mode. Long primer RAPD (randomly amplified polymorphic DNA) community fingerprints of the anoxic reactor also changed most significantly from the one similar to the anaerobic reactor to one similar to the oxic reactor. DNA hybridization revealed one signature band of 2.1 kb shared by the anoxic and oxic reactors in LR, but not LNR mode. Clone library profiling of this band resulted in one predominant 2.1-kb genomic fragment (B3) with no homologous sequences in GenBank. Real-time polymerase chain reaction indicated that copy numbers of B3 in the anoxic reactor under LR mode were 69 times higher than that under LNR mode, concomitant to a significant increase in COD removal capacity in this reactor. The different patterns of distribution of B3 in the laboratory system and a comparable malfunctioning industrial system demonstrated the potential of this genomic fragment as physical markers in systems monitoring. In addition, this genomic fragment may allow sequence-guided isolation of the host microbe.

GH97 is a new family of glycoside hydrolases, which is related to the alpha-galactosidase superfamily

Background

As a rule, about 1% of genes in a given genome encode glycoside hydrolases and their homologues. On the basis of sequence similarity they have been grouped into more than ninety GH families during the last 15 years. The GH97 family has been established very recently and initially included only 18 bacterial proteins. However, the evolutionary relationship of the genes encoding proteins of this family remains unclear, as well as their distribution among main groups of the living organisms.

Results

The extensive search of the current databases allowed us to double the number of GH97 family proteins. Five subfamilies were distinguished on the basis of pairwise sequence comparison and phylogenetic analysis. Iterative sequence analysis revealed the relationship of the GH97 family with the GH27, GH31, and GH36 families of glycosidases, which belong to the α-galactosidase superfamily, as well as a more distant relationship with some other glycosidase families (GH13 and GH20).

Conclusion

The results of this study show an unexpected sequence similarity of GH97 family proteins with glycoside hydrolases from several other families, that have (β/α)₈-barrel fold of the catalytic domain and a retaining mechanism of the glycoside bond hydrolysis. These data suggest a common evolutionary origin of glycosidases representing different families and clans.

Molecular profiling of Bacteroides spp. in human feces by PCR-temperature gradient gel electrophoresis

A group-specific PCR-based temperature gradient gel electrophoresis (TGGE) method was developed to study the population composition of genus Bacteroides in human gut. Highly reproducible and well-separated bands in TGGE fingerprints of ten unrelated human fecal samples showed complex and host-specific Bacteroides species composition. Dynamic monitoring over 22 months of samples from one healthy 10-year-old boy indicated a relatively stable population profile of Bacteroides. The species identity of each band in TGGE gel of this boy was also resolved via comigration analysis of sequenced inserts in a Bacteroides group-specific clone library. This work provides a rapid and effective technique for analyzing the species composition of Bacteroides in human gut.