Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns

Effects of dietary resistant starch content on metabolic status, milk composition, and microbial profiling in lactating sows and on offspring performance

In the present study, the effects of dietary resistant starch (RS) content on serum metabolite and hormone concentrations, milk composition, and faecal microbial profiling in lactating sows, as well as on offspring performance was investigated. Sixteen sows were randomly allotted at breeding to two treatments containing low- and high-RS contents from normal and high-amylose corn varieties, respectively, and each treatment had eight replicates (sows). Individual piglet body weight (BW) and litter size were recorded at birth and weaning. Milk samples were obtained on day 10 after farrowing for composition analysis. On day 2 before weaning, blood and faecal samples were collected to determine serum metabolite and hormone concentrations and faecal microbial populations, respectively. Litter size at birth and weaning were not influenced (p > 0.05) by the sow dietary treatments. Although feeding the RS-rich diet to sows reduced (p = 0.004) offspring birth BW, there was no difference in piglet BW at weaning (p > 0.05). High-RS diet increased (p < 0.05) serum triacylglycerol and nonesterified fatty acid concentrations and milk total solid content, and tended (p = 0.09) to increase milk fat content in lactating sows. Feeding the RS-rich diet to sows increased (p < 0.01) faecal bacterial population diversity. These results indicate that high-RS diets induce fatty acid mobilization and a greater intestinal bacterial richness in lactating sows, as well as a greater nutrient density in maternal milk, without affecting offspring performance at weaning.

Sanitary impact evaluation of drinking water in storage reservoirs in Moroccan rural area

In Morocco, storage reservoirs are particular systems of water supply in rural areas. These reservoirs are fed with rainwater and/or directly from the river, which are very contaminated by several pathogenic bacteria. They are used without any treatment as a drinking water by the surrounding population. In this context, the aim of this study is to evaluate the impact of consuming contaminated water stored in reservoirs on health status for six rural communities located in Assif El Mal, Southern East of Marrakech. This was investigated using a classical methodology based on population survey and by molecular approach using PCR–DGGE technique to determine the intestinal bacterial diversity of consumers. The survey showed that, the residents of the studied area suffered from numerous health problems (diarrheal diseases, vomiting or hepatitis A) due to the lack of waste management infrastructures. The consumer’s stool analysis by molecular approach revealed that numbers of Escherichia coli, Aeromonas hydrophila and Clostridia, were significantly higher in the diarrheal feces. In addition, PCR–DGGE study of the prevalence and distribution of bacteria causing human diseases, confirmed that, there is a relationship between water bacterial contaminations of storage reservoirs and microbial disease related health status. Therefore, water reservoir consumption is assumed to be the mean way of exposure for this population.

It’s clear that this approach gives a very helpful tool to confirm without any doubt the relationship between water bacterial contamination and health status.

Microbial responses to polycyclic aromatic hydrocarbon contamination in temporary river sediments: Experimental insights

Temporary rivers are characterized by dry-wet phases and represent an important water resource in semi-arid regions worldwide. The fate and effect of contaminants have not been firmly established in temporary rivers such as in other aquatic environments. In this study, we assessed the effects of sediment amendment with Polycyclic Aromatic Hydrocarbons (PAHs) on benthic microbial communities. Experimental microcosms containing natural (Control) and amended sediments (2 and 20 mg PAHs kg(-1) were incubated for 28 days. The PAH concentrations in sediments were monitored weekly together with microbial community structural (biomass and phylogenetic composition by TGGE and CARD-FISH) and functional parameters (ATP concentration, community respiration rate, bacterial carbon production rate, extracellular enzyme activities). The concentration of the PAH isomers did not change significantly with the exception of phenanthrene. No changes were observed in the TGGE profiles, whereas the occurrence of Alpha- and Beta-Proteobacteria was significantly affected by the treatments. In the amended sediments, the rates of carbon production were stimulated together with aminopeptidase enzyme activity. The community respiration rates showed values significantly lower than the Control after 1 day from the amendment then recovering the Control values during the incubation. A negative trend between the respiration rates and ATP concentration was observed only in the amended sediments. This result indicates a potential toxic effect on the oxidative phosphorylation processes. The impoverishment of the energetic resources that follows the PAH impact may act as a domino on the flux of energy from prokaryotes to the upper level of the trophic chain, with the potential to alter the temporary river functioning.

Cry1Ac Transgenic Sugarcane Does Not Affect the Diversity of Microbial Communities and Has No Significant Effect on Enzyme Activities in Rhizosphere Soil within One Crop Season

Cry1Ac transgenic sugarcane provides a promising way to control stem-borer pests. Biosafety assessment of soil ecosystem for cry1Ac transgenic sugarcane is urgently needed because of the important role of soil microorganisms in nutrient transformations and element cycling, however little is known. This study aimed to explore the potential impact of cry1Ac transgenic sugarcane on rhizosphere soil enzyme activities and microbial community diversity, and also to investigate whether the gene flow occurs through horizontal gene transfer. We found no horizontal gene flow from cry1Ac sugarcane to soil. No significant difference in the population of culturable microorganisms between the non-GM and cry1Ac transgenic sugarcane was observed, and there were no significant interactions between the sugarcane lines and the growth stages. A relatively consistent trend at community-level, represented by the functional diversity index, was found between the cry1Ac sugarcane and the non-transgenic lines. Most soil samples showed no significant difference in the activities of four soil enzymes: urease, protease, sucrose, and acid phosphate monoester between the non-transgenic and cry1Ac sugarcane lines. We conclude, based on one crop season, that the cry1Ac sugarcane lines may not affect the microbial community structure and functional diversity of the rhizosphere soil and have few negative effects on soil enzymes.

Bacterial concentration and diversity in fresh tropical shrimps (Penaeus notialis) and the surrounding brackish waters and sediment

This study aimed at determining bacterial concentration and diversity in fresh tropical shrimps (Penaeus notialis) and their surrounding brackish waters and sediment. Freshly caught shrimp, water and sediment samples were collected in Lakes Nokoue and Aheme in Benin (West Africa) during two periods with different water salinity and temperature. We used complementary culture-dependent and culture-independent methods for microbiota analysis. During both sampling periods, total mesophilic aerobic counts in shrimp samples ranged between 4.4 and 5.9 log CFU/g and were significantly higher than in water or sediment samples. In contrast, bacterial diversity was higher in sediment or water than in shrimps. The dominant phyla were Firmicutes and Proteobacteria in shrimps, Firmicutes, Proteobacteria, and Actinobacteria in water, and Proteobacteria and Chloroflexi in sediment. At species level, distinct bacterial communities were associated with sediment, water and shrimps sampled at the same site the same day. The study suggests that the bacterial community of tropical brackish water shrimps cannot be predicted from the microbiota of their aquatic environment. Thus, monitoring of microbiological quality of aquatic environments might not reflect shrimp microbiological quality.

Fungal community dynamics and driving factors during agricultural waste composting

This study was conducted to identify the driving factors behind fungal community dynamics during agricultural waste composting. Fungal community abundance and structure were determined by quantitative PCR and denaturing gradient gel electrophoresis analysis combined with DNA sequencing. The effects of physico-chemical parameters on fungal community abundance and structure were evaluated by least significant difference tests and redundancy analysis. The results showed that Cladosporium bruhnei, Hanseniaspora uvarum, Scytalidium thermophilum, Tilletiopsis penniseti, and Coprinopsis altramentaria were prominent during the composting process. The greatest variation in the distribution of fungal community structure was statistically explained by pile temperature and total organic carbon (TOC) (P < 0.05). A significant amount of the variation (74.6 %) was explained by these two parameters alone. Fungal community abundance was found to be significantly related to pH, while pH was significantly influenced by pile temperature and nitrate levels (P < 0.05), and these parameters were found to be the most likely to influence or be influenced by the fungal community during composting.

Nutrient-cycling microbes in coastal Douglas-fir forests: regional-scale correlation between communities, in situ climate, and other factors

Microbes such as fungi and bacteria play fundamental roles in litter-decay and nutrient-cycling; however, their communities may respond differently than plants to climate change. The structure (diversity, richness, and evenness) and composition of microbial communities in climate transects of mature Douglas-fir stands of coastal British Columbia rainshadow forests was analyzed, in order to assess in situ variability due to different temperature and moisture regimes. We compared denaturing gradient gel electrophoresis profiles of fungi (18S-FF390/FR1), nitrogen-fixing bacteria (NifH-universal) and ammonia-oxidizing bacteria (AmoA) polymerase chain reaction amplicons in forest floor and mineral soil samples from three transects located at different latitudes, each transect spanning the Coastal Western Hemlock and Douglas-fir biogeoclimatic zones. Composition of microbial communities in both soil layers was related to degree days above 0°C (2725–3489), while pH (3.8–5.5) best explained shifts in community structure. At this spatial scale, climatic conditions were likely to directly or indirectly select for different microbial species while local site heterogeneity influenced community structure. Significant changes in microbial community composition and structure were related to differences as small as 2.47% and 2.55°C in mean annual moisture and temperature variables, respectively. The climatic variables best describing microbial composition changed from one functional group to the next; in general they did not alter community structure. Spatial distance, especially associated with latitude, was also important in accounting for community variability (4–23%); but to a lesser extent than the combined influence of climate and soil characteristics (14–25%). Results suggest that in situ climate can independently account for some patterns of microbial biogeography in coastal Douglas-fir forests. The distribution of up to 43% of nutrient-cycling microorganisms detected in forest soils responded to smaller abiotic gradients than host trees.

Dynamics of bacterial assemblages and removal of polycyclic aromatic hydrocarbons in oil-contaminated coastal marine sediments subjected to contrasted oxygen regimes

To study the impact of oxygen regimes on the removal of polycylic aromatic hydrocarbons (PAHs) in oil-spill-affected coastal marine sediments, we used a thin-layer incubation method to ensure that the incubated sediment was fully oxic, anoxic, or was influenced by oxic-anoxic switches without sediment stirring. Hydrocarbon content and microbial assemblages were followed during 60 days to determine PAH degradation kinetics and microbial community dynamics according to the oxygenation regimes. The highest PAH removal, with 69 % reduction, was obtained at the end of the experiment under oxic conditions, whereas weaker removals were obtained under oscillating and anoxic conditions (18 and 12 %, respectively). Bacterial community structure during the experiment was determined using a dual 16S rRNA genes/16S rRNA transcripts approach, allowing the characterization of metabolically active bacteria responsible for the functioning of the bacterial community in the contaminated sediment. The shift of the metabolically active bacterial communities showed that the selection of first responders belonged to Pseudomonas spp. and Labrenzia sp. and included an unidentified Deltaproteobacteria-irrespective of the oxygen regime-followed by the selection of late responders adapted to the oxygen regime. A novel unaffiliated phylotype (B38) was highly active during the last stage of the experiment, at which time, the low-molecular-weight (LMW) PAH biodegradation rates were significant for permanent oxic- and oxygen-oscillating conditions, suggesting that this novel phylotype plays an active role during the restoration phase of the studied ecosystem.

Modulation of immunity and gut microbiota after dietary administration of alginate encapsulated Shewanella putrefaciens Pdp11 to gilthead seabream (Sparus aurata L.)

The potential benefits of probiotics when administering to fish could improve aquaculture production. The objective of this study was to examine the modulation of immune status and gut microbiota of gilthead seabream (Sparus aurata L.) specimens by a probiotic when administered encapsulated. Commercial diet was enriched with Shewanella putrefaciens Pdp11 (SpPdp11, at a concentration of 10(8) cfu g(-1)) before being encapsulated in calcium alginate beads. Fish were fed non-supplemented (control) or supplemented diet for 4 weeks. After 1, 2 and 4 weeks the main humoral and cellular immune parameters were determined. Furthermore, gene expression profile of five immune relevant genes (il1β, bd, mhcIIα, ighm and tcrβ) was studied by qPCR in head kidney. On the other hand, intestinal microbiota of fish was analysed at 7 and 30 days by DGGE. Results demonstrated that administration of alginate encapsulated SpPdp11 has immunostimulant properties on humoral parameters (IgM level and serum peroxidase activity). Although no immunostimulant effects were detected on leucocyte activities, significant increases were detected in the level of mRNA of head-kidney leucocytes for mhcIIα and tcrβ after 4 weeks of feeding the encapsulated-probiotic diet. The administration of SpPdp11 encapsulated in alginate beads produced important changes in the DGGE patterns corresponding to the intestinal microbiota. Predominant bands related to lactic acid bacteria, such as Lactococcus and Lactobacillus strains, were sequenced from the DGGE patterns of fish fed the probiotic diet, whereas they were not sequenced from fish receiving the control diet. The convenience or not of probiotic encapsulation is discussed.

Association of oral streptococci community dynamics with severe early childhood caries as assessed by PCR-denaturing gradient gel electrophoresis targeting the rnpB gene

This study sought to investigate the possible association between the dynamics of oral streptococci community profiles and severe early childhood caries (S-ECC) development, compared with caries-free (CF) controls. Supragingival plaque samples were evaluated from 8-32-month-old children who had previously been assessed for overall profiles of their oral microbial community. Twelve children were in each group. Bacterial genomic DNA was extracted and amplified using rnpB-specific primers for streptococci; the products were then subjected to denaturing gradient gel electrophoresis (DGGE) and sequence analysis. We observed that the mean values for species richness (N) and diversity of oral streptococci (H') were significantly lower in the S-ECC group than in the CF group (N = 1.25 ± 4.14 vs 14.92 ± 2.84; H' = 1.41 ± 0.29 vs 1.64 ± 0.18) at 32  months of age (P < 0.05). Significantly higher detection rates of Streptococcus sanguinis and Streptococcus gordonii were found in the CF group compared with the S-ECC group at 32  months of age (P < 0.05). Cluster analysis of DGGE profiles showed that most of the clusters were constructed from one individual over time. These results suggested that the onset of S-ECC is accompanied by reduced diversity of oral streptococci, that the detection rates of S. sanguinis and S. gordonii have negative correlations with S-ECC; and that there are high levels of intra-individual similarity for the oral streptococci community over time.

Distribution and diversity of fungi in freshwater sediments on a river catchment scale

Fungal communities perform essential functions in biogeochemical cycles. However, knowledge of fungal community structural changes in river ecosystems is still very limited. In the present study, we combined culture-dependent and culture-independent methods to investigate fungal distribution and diversity in sediment on a regional scale in the Songhua River catchment, located in North-East Asia. A total of 147 samples over the whole river catchment were analyzed. The results showed that compared to the mainstream, the tributaries have a higher fungal community organization and culturable fungal concentration, but possess lower community dynamics as assessed by denaturing gradient gel electrophoresis (DGGE). Furthermore, phylogenetic analysis of DGGE bands showed that Ascomycota and Basidiomycota were the predominant community in the Songhua River catchment. Redundancy analysis revealed that longitude was the primary factor determining the variation of fungal community structure, and fungal biomass was mainly related to the total nutrient content. Our findings provide new insights into the characteristics of fungal community distribution in a temperate zone river at a regional scale, and demonstrate that fungal dispersal is restricted by geographical barriers in a whole river catchment.

The abundance of functional genes, cbbL, nifH, amoA and apsA, and bacterial community structure of intertidal soil from Arabian Sea

The Gulf of Cambay is a trumpet-shaped inlet of the Arabian Sea, located along the west coast of India and confronts a high tidal range with strong water currents. The region belongs to a semi-arid zone and saline alkaline intertidal soils are considered biologically extreme. The selected four soil types (S1-S4) were affected by salinity, alkalinity and sodicity. Soil salinity ranged from 20 to 126 dS/m, soil pH 8.6-10.0 with high sodium adsorption ratio (SAR) and exchangeable sodium percentage (ESP). Abundance of the key functional genes like cbbL, nifH, amoA and apsA involved in biogeochemical cycling were targeted using qPCR, which varied from (2.36 ± 0.03) × 10(4) to (2.87 ± 0.26) × 10(8), (1.18 ± 0.28) × 10(6) to (1.01 ± 0.26) × 10(9), (1.41 ± 0.21) × 10(6) to (1.29 ± 0.05) × 10(8) and (8.47 ± 0.23) × 10(4) to (1.73 ± 0.01) × 10(6) per gram dry weight, respectively. The microbial community structure revealed that soils S1 and S3 were dominated by phylum Firmicutes whereas S4 and S2 showed an abundance of Proteobacterial clones. These soils also represented Bacteroidetes, Chloroflexi, Actinobacteria, Planctomycetes and Acidobacteria clones. Molecular phylogeny showed a significant variation in the bacterial community distribution among the intertidal soil types. A high number of novel taxonomic units were observed which makes the intertidal zone a unique reservoir of unidentified bacterial taxa that may be explored further.

Sponging up metals: bacteria associated with the marine sponge Spongia officinalis

The present study explored the bacteria of the sponge Spongia officinalis in a metal-polluted environment, using PCR-DGGE fingerprinting, culture-dependent approaches and in situ hybridization. The sponge samples collected over three consecutive years in the Western Mediterranean Sea contained high concentrations of zinc, nickel, lead and copper determined by ICP-MS. DGGE signatures indicated a sponge specific bacterial association and suggested spatial and temporal variations. The bacterial culturable fraction associated with S. officinalis and tolerant to heavy metals was isolated using metal-enriched microbiological media. The obtained 63 aerobic strains were phylogenetically affiliated to the phyla Proteobacteria, Actinobacteria, and Firmicutes. All isolates showed high tolerances to the selected heavy metals. The predominant genus Pseudovibrio was localized via CARD-FISH in the sponge surface tissue and validated as a sponge-associated epibiont. This study is the first step in understanding the potential involvement of the associated bacteria in sponge's tolerance to heavy metals.

Study of phenanthrene utilizing bacterial consortia associated with cowpea (Vigna unguiculata) root nodules

Many legumes have been selected as model plants to degrade organic contaminants with their special associated rhizosphere microbes in soil. However, the function of root nodules during microbe-assisted phytoremediation is not clear. A pot study was conducted to examine phenanthrene (PHE) utilizing bacteria associated with root nodules and the effects of cowpea root nodules on phytoremediation in two different types of soils (freshly contaminated soil and aged contaminated soil). Cowpea nodules in freshly-contaminated soil showed less damage in comparison to the aged-contaminated soil, both morphologically and ultra-structurally by scanning electron microscopy. The study of polycyclic aromatic hydrocarbon (PAH) attenuation conducted by high performance liquid chromatography revealed that more PAH was eliminated from liquid culture around nodulated roots than nodule-free roots. PAH sublimation and denaturation gradient gel electrophoresis were applied to analyze the capability and diversity of PAH degrading bacteria from the following four parts of rhizo-microzone: bulk soil, root surface, nodule surface and nodule inside. The results indicated that the surface and inside of cowpea root nodules were colonized with bacterial consortia that utilized PHE. Our results demonstrated that root nodules not only fixed nitrogen, but also enriched PAH-utilizing microorganisms both inside and outside of the nodules. Legume nodules may have biotechnological values for PAH degradation.

Rapid fingerprinting of methanogenic communities by high-resolution melting analysis

Characterizing microbial community structure using molecular techniques is becoming a popular approach in studies of waste/wastewater treatment processes. A rapid and robust tool to analyze microbial communities is required for efficient process monitoring and control. In this study, a new community fingerprinting method based on high-resolution melting (HRM) analysis was developed and applied to compare methanogenic community structures of five different anaerobic digesters. The new method produced robust community clustering and ordination results comparable to the results from the commonly used denaturing gradient gel electrophoresis (DGGE) performed in parallel. This method transforms melting peak plots (MPs) of community DNA samples generated by HRM analysis to molecular fingerprints and estimates the relationships between the communities based on the fingerprints. The MP-based fingerprinting would provide a good alternative to monitor variations in microbial community structure especially when handling large sample numbers due to its high-throughput capacity and short analysis time.

The treatment with the probiotic Shewanella putrefaciens Pdp11 of specimens of Solea senegalensis exposed to high stocking densities to enhance their resistance to disease

Aquaculture industry exposes fish to acute stress events, such as high stocking density, and a link between stress and higher susceptibility to diseases has been concluded. Several studies have demonstrated increased stress tolerance of fish treated with probiotics, but the mechanisms involved have not been elucidated. Shewanella putrefaciens Pdp11 is a strain isolated from healthy gilthead seabream (Sparus aurata L.) and it is considered as probiotics. The aim of this study was to evaluate the effect of the dietary administration of this probiotics on the stress tolerance of Solea senegalensis specimens farmed under high stocking density (PHD) compared to a group fed a commercial diet and farmed under the same conditions (CHD). In addition, during the experiment, a natural infectious outbreak due to Vibrio species affected fish farmed under crowding conditions. Changes in the microbiota and histology of intestine and in the transcription of immune response genes were evaluated at 19 and 30 days of the experiment. Mortality was observed after 9 days of the beginning of the experiment in CHD and PHD groups, it being higher in the CHD group. Fish farmed under crowding stress showed reduced expression of genes at 19 day probiotic feeding. On the contrary, a significant increase in immune related gene expression was detected in CHD fish at 30 day, whereas the gene expression in fish from PHD group was very similar to that showed in specimens fed and farmed with the conventional conditions. In addition, the dietary administration of S. putrefaciens Pdp11 produced an important modulation of the intestinal microbiota, which was significantly correlated with the high number of goblet cells detected in fish fed the probiotic diet.

Analysis of the bacterial community in chronic obstructive pulmonary disease sputum samples by denaturing gradient gel electrophoresis and real-time PCR

Background

The Global Initiative defines COPD for chronic obstructive lung disease as an entirely preventable and treatable disease characterized by sputum production, bacterial colonisation, neutrophilic bronchial airway inflammation and poor health status. The World Health Organization (WHO) estimates that COPD will become the fourth-most common cause of death worldwide, just behind ischemic heart disease, cerebrovascular disease and HIV/AIDS, by 2030. The aim of this study was to determine the main structure feature of sputum potentially pathogenic microorganisms in subjects with COPD during the clinical stable state.

Methods

We employed a molecular genetics-based investigation of the bacteria community, including DNA isolation, PCR amplification and DGGE profiling. PCR-denaturing gradient gel electrophoresis (DGGE) with universal primers targeting the V3 region of the 16S rRNA gene was employed to characterize the overall COPD patient sputum microbiota composition, and some excised gel bands were cloned for sequencing. Real-time PCR was further utilized to quantitatively analyze the subpopulation of microbiota using group-specific primers targeting Streptococcus pneumoniae, Klebsiella pneumoniae, Pseudomonas aeruginosa.

Results

The DGGE profiles of two groups displayed significant differences between COPD and healthy groups (P < 0.05). Real-time PCR revealed significant increases of Streptococcus pneumoniae, Klebsiella pneumoniae and Pseudomonas aeruginosa (P < 0.05) in the COPD group compared with the healthy group.

Conclusion

This study revealed strong relationship between alterations of sputum microbiota and COPD. By determining the content of several types of bacteria, we can provide evidence to aid in the diagnosis and treatment of COPD.

Effect of organic food and moxibustion on diversity of rat gut microbiota

AIM: To compare the effect of organic and conventional food on the diversity of rat gut microbiota and to observe the changes in the composition of gut microbiota after moxibustion at Zusanli and Piyu points.

METHODS: Twenty-four SD rats of SPF grade were randomly divided into three groups: an organic food group, a conventional food group and a conventional food + moxibustion group. The mice of the organic food group were fed organic food for 12 wk, the mice of the convention food group were fed conventional food for 12 wk, and the combination group were fed conventional food for 8 wk and given moxibustion at Zusanli and Piyu points for additional 4 wk. The changes in gut microbiota were analyzed by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE).

RESULTS: The similarity clustering analysis showed that the composition of gut microbiota had significant differences among the three groups. The gut bacterial diversity index in the combination group significantly increased (P < 0.05). DNA sequencing showed that organic diet promoted Bacteroides stercoris to bloom in the gut of mice, and Moxibustion at Zusanli and Piyu points promoted the multiplication of Barnesiella intestinihominis and Bacteroides stercoris.

CONCLUSION: Organic diet and moxibustion obviously increase gut bacterial diversity index, and Moxibustion has a more significant effect. Organic diet is conducive to the stability of the intestinal flora. If organic diet cannot be ensured, moxibustion at Zusanli and Piyu points is helpful.

Importance of Rhodococcus strains in a bacterial consortium degrading a mixture of hydrocarbons, gasoline, and diesel oil additives revealed by metatranscriptomic analysis

A bacterial consortium (Mix3) composed of microorganisms originating from different environments (soils and wastewater) was obtained after enrichment in the presence of a mixture of 16 hydrocarbons, gasoline, and diesel oil additives. After addition of the mixture, the development of the microbial composition of Mix3 was monitored at three different times (35, 113, and 222 days) using fingerprinting method and dominant bacterial species were identified. In parallel, 14 bacteria were isolated after 113 days and identified. Degradation capacities for Mix3 and the isolated bacterial strains were characterized and compared. At day 113, we induced the expression of catabolic genes in Mix3 by adding the substrate mixture to resting cells and the metatranscriptome was analyzed. After addition of the substrate mixture, the relative abundance of Actinobacteria increased at day 222 while a shift between Rhodococcus and Mycobacterium was observed after 113 days. Mix3 was able to degrade 13 compounds completely, with partial degradation of isooctane and 2-ethylhexyl nitrate, but tert-butyl alcohol was not degraded. Rhodococcus wratislaviensis strain IFP 2016 isolated from Mix3 showed almost the same degradation capacities as Mix3: these results were not observed with the other isolated strains. Transcriptomic results revealed that Actinobacteria and in particular, Rhodococcus species, were major contributors in terms of total and catabolic gene transcripts while other species were involved in cyclohexane degradation. Not all the microorganisms identified at day 113 were active except R. wratislaviensis IFP 2016 that appeared to be a major player in the degradation activity observed in Mix3.

Structure and microbial diversity of biofilms on different pipe materials of a model drinking water distribution systems

The experiment was conducted in three model drinking water distribution systems (DWDSs) made of unplasticized polyvinyl chloride (PVC), silane cross-linked polyethylene (PEX) and high density polyethylene (HDPE) pipes to which tap water was introduced. After 2 years of system operation, microbial communities in the DWDSs were characterized with scanning electron microscopy, heterotrophic plate count, and denaturing gradient gel electrophoresis. The most extensive biofilms were found in HDPE pipes where bacteria were either attached to mineral deposits or immersed in exopolymers. On PEX surfaces, bacteria did not form large aggregates; however, they were present in the highest number (1.24 × 10⁷ cells cm⁻²). PVC biofilm did not contain mineral deposits but was made of single cells with a high abundance of Pseudomonas aeruginosa, which can be harmful to human health. The members of Proteobacteria and Bacteroidetes were found in all biofilms and the water phase. Sphingomonadales and Methylophilaceae bacteria were found only in PEX samples, whereas Geothrix fermentans, which can reduce Fe(III), were identified only in PEX biofilm. The DNA sequences closely related to the members of Alphaproteobacteria were the most characteristic and intense amplicons detected in the HDPE biofilm.

Effect of Feeding Bacillus subtilis natto on Hindgut Fermentation and Microbiota of Holstein Dairy Cows

The effect of Bacillus subtilis natto on hindgut fermentation and microbiota of early lactation Holstein dairy cows was investigated in this study. Thirty-six Holstein dairy cows in early lactation were randomly allocated to three groups: no B. subtilis natto as the control group, B. subtilis natto with 0.5×10(11) cfu as DMF1 group and B. subtilis natto with 1.0×10(11) cfu as DMF2 group. After 14 days of adaptation period, the formal experiment was started and lasted for 63 days. Fecal samples were collected directly from the rectum of each animal on the morning at the end of eighth week and placed into sterile plastic bags. The pH, NH3-N and VFA concentration were determined and fecal bacteria DNA was extracted and analyzed by DGGE. The results showed that the addition of B. subtilus natto at either treatment level resulted in a decrease in fecal NH3-N concentration but had no effect on fecal pH and VFA. The DGGE profile revealed that B. subtilis natto affected the population of fecal bacteria. The diversity index of Shannon-Wiener in DFM1 decreased significantly compared to the control. Fecal Alistipes sp., Clostridium sp., Roseospira sp., beta proteobacterium were decreased and Bifidobacterium was increased after supplementing with B. subtilis natto. This study demonstrated that B. subtilis natto had a tendency to change fecal microbiota balance.

Pros and cons of ion-torrent next generation sequencing versus terminal restriction fragment length polymorphism T-RFLP for studying the rumen bacterial community

The development of next generation sequencing has challenged the use of other molecular fingerprinting methods used to study microbial diversity. We analysed the bacterial diversity in the rumen of defaunated sheep following the introduction of different protozoal populations, using both next generation sequencing (NGS: Ion Torrent PGM) and terminal restriction fragment length polymorphism (T-RFLP). Although absolute number differed, there was a high correlation between NGS and T-RFLP in terms of richness and diversity with R values of 0.836 and 0.781 for richness and Shannon-Wiener index, respectively. Dendrograms for both datasets were also highly correlated (Mantel test = 0.742). Eighteen OTUs and ten genera were significantly impacted by the addition of rumen protozoa, with an increase in the relative abundance of Prevotella, Bacteroides and Ruminobacter, related to an increase in free ammonia levels in the rumen. Our findings suggest that classic fingerprinting methods are still valuable tools to study microbial diversity and structure in complex environments but that NGS techniques now provide cost effect alternatives that provide a far greater level of information on the individual members of the microbial population.

Remediation of phenanthrene-contaminated soil by simultaneous persulfate chemical oxidation and biodegradation processes

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous compounds with carcinogenic and/or mutagenic potential. To address the limitations of individual remediation techniques and to achieve better PAH removal efficiencies, the combination of chemical and biological treatments can be used. The degradation of phenanthrene (chosen as a model of PAH) by persulfate in freshly contaminated soil microcosms was studied to assess its impact on the biodegradation process and on soil properties. Soil microcosms contaminated with 140 mg/kgDRY SOIL of phenanthrene were treated with different persulfate (PS) concentrations 0.86-41.7 g/kgDRY SOIL and incubated for 28 days. Analyses of phenanthrene and persulfate concentrations and soil pH were performed. Cultivable heterotrophic bacterial count was carried out after 28 days of treatment. Genetic diversity analysis of the soil microcosm bacterial community was performed by PCR amplification of bacterial 16S rDNA fragments followed by denaturing gradient gel electrophoresis (DGGE). The addition of PS in low concentrations could be an interesting biostimulatory strategy that managed to shorten the lag phase of the phenanthrene biological elimination, without negative effects on the physicochemical and biological soil properties, improving the remediation treatment.

Assessing genetic diversity among Brettanomyces yeasts by DNA fingerprinting and whole-genome sequencing

Brettanomyces yeasts, with the species Brettanomyces (Dekkera) bruxellensis being the most important one, are generally reported to be spoilage yeasts in the beer and wine industry due to the production of phenolic off flavors. However, B. bruxellensis is also known to be a beneficial contributor in certain fermentation processes, such as the production of certain specialty beers. Nevertheless, despite its economic importance, Brettanomyces yeasts remain poorly understood at the genetic and genomic levels. In this study, the genetic relationship between more than 50 Brettanomyces strains from all presently known species and from several sources was studied using a combination of DNA fingerprinting techniques. This revealed an intriguing correlation between the B. bruxellensis fingerprints and the respective isolation source. To further explore this relationship, we sequenced a (beneficial) beer isolate of B. bruxellensis (VIB X9085; ST05.12/22) and compared its genome sequence with the genome sequences of two wine spoilage strains (AWRI 1499 and CBS 2499). ST05.12/22 was found to be substantially different from both wine strains, especially at the level of single nucleotide polymorphisms (SNPs). In addition, there were major differences in the genome structures between the strains investigated, including the presence of large duplications and deletions. Gene content analysis revealed the presence of 20 genes which were present in both wine strains but absent in the beer strain, including many genes involved in carbon and nitrogen metabolism, and vice versa, no genes that were missing in both AWRI 1499 and CBS 2499 were found in ST05.12/22. Together, this study provides tools to discriminate Brettanomyces strains and provides a first glimpse at the genetic diversity and genome plasticity of B. bruxellensis.

Specificity and temporal dynamics of complex bacteria--sponge symbiotic interactions

Microbes are known to form intricate and intimate relationships with most animal and plant taxa. Microbe--host symbiotic associations are poorly explored in comparison with other species interaction networks. The current paradigm on symbiosis research stems from species-poor systems where pairwise and reciprocally specialized interactions between a single microbe and a single host that coevolve are the norm. These symbioses involving just a few species are fascinating in their own right, but more diverse and complex host-associated microbial communities are increasingly found, with new emerging questions that require new paradigms and approaches. Here we adopt an intermediate complexity approach to study the specificity, phylogenetic community structure, and temporal variability of the subset of the most abundant bacteria associated with different sponge host species with diverse eco-evolutionary characteristics. We do so by using a monthly resolved annual temporal series of host-associated and free-living bacteria. Bacteria are very abundant and diverse within marine sponges, and these symbiotic interactions are hypothesized to have a very ancient origin. We show that host-bacteria reciprocal specialization depends on the temporal scale and level of taxonomic aggregation considered. Sponge hosts with similar eco-evolutionary characteristics (e.g., volume of tissue corresponding to microbes, water filtering rates, and microbial transmission type) have similar bacterial phylogenetic community structure when looking at interactions aggregated over time. In general, sponge hosts hypothesized to form more intricate relationships with bacteria show a remarkably persistent bacterial community over time. Other hosts, however, show a large turnover similar to that observed for free-living bacterioplankton. Our study highlights the importance of exploring temporal variability in host--microbe interaction networks if we aim to determine how specific and persistent these poorly explored but extremely common interactions are.

Distinct polymicrobial populations in a chronic foot ulcer with implications for diagnostics and anti-infective therapy

Background

Polymicrobial infections caused by combinations of different bacteria are being detected with an increasing frequency. The evidence of such complex infections is being revealed through the use of novel molecular and culture-independent methods. Considerable progress has been made in the last decade regarding the diagnostic application of such molecular techniques. In particular, 16S rDNA-based sequencing and even metagenomic analyses have been successfully used to study the microbial diversity in ecosystems and human microbiota. Here, we utilized denaturing high-performance liquid chromatography (DHPLC) as a diagnostic tool for identifying different bacterial species in complex clinical samples of a patient with a chronic foot ulcer.

Case presentation

A 45-year-old female suffered from a chronic 5x5cm large plantar ulcer located in the posterior calcaneal area with subcutaneous tissue infection and osteomyelitis. The chronic ulcer developed over a period of 8 years. Culture and DHPLC revealed a distinct and location-dependent polymicrobial infection of the ulcer. The analysis of a superficial biopsy revealed a mixture of Staphylococcus aureus, Proteus vulgaris, and Fusobacterium nucleatum, whereas the tissue-deep biopsy harbored a mixture of four different bacterial species, namely Gemella morbillorum, Porphyromonas asaccharolytica, Bacteroides fragilis, and Arcanobacterium haemolyticum.

Conclusions

This clinical case highlights the difficulties in assessing polymicrobial infections where a mixture of fastidious, rapid and slow growing bacteria as well as anaerobes exists as structured communities within the tissue architecture of chronic wound infections. The diagnosis of this multilayered polymicrobial infection led to a microbe-adapted antibiotic therapy, targeting the polymicrobial nature of this infection in addition to a standard local wound treatment. However, a complete wound closure could not be achieved due to the long-lasting extensive destruction of tissue.

Prospecting metal-resistant plant-growth promoting rhizobacteria for rhizoremediation of metal contaminated estuaries using Spartina densiflora

In the salt marshes of the joint estuary of Tinto and Odiel rivers (SW Spain), one of the most polluted areas by heavy metals in the world, Spartina densiflora grows on sediments with high concentrations of heavy metals. Furthermore, this species has shown to be useful for phytoremediation. The total bacterial population of the rhizosphere of S. densiflora grown in two estuaries with different levels of metal contamination was analyzed by PCR denaturing gradient gel electrophoresis. Results suggested that soil contamination influences bacterial population in a greater extent than the presence of the plant. Twenty-two different cultivable bacterial strains were isolated from the rhizosphere of S. densiflora grown in the Tinto river estuary. Seventy percent of the strains showed one or more plant growth-promoting (PGP) properties, including phosphate solubilization and siderophores or indolacetic acid production, besides a high resistance towards Cu. A bacterial consortium with PGP properties and very high multiresistance to heavy metals, composed by Aeromonas aquariorum SDT13, Pseudomonas composti SDT3, and Bacillus sp. SDT14, was selected for further experiments. This consortium was able to two-fold increase seed germination and to protect seeds against fungal contamination, suggesting that it could facilitate the establishment of the plant in polluted estuaries.

Compositional differences in fecal microbiota between rats with colorectal cancer and normal rats

AIM: To investigate the compositional differences in fecal flora between rats with colorectal cancer and normal rats.

METHODS: A rat model of colorectal cancer was developed by intraperitoneal injection of 1, 2-dimethyl hydrazine (DMH). Fecal samples were collected from rats with colorectal cancer and normal controls, and the microbiota was isolated by PCR-DGGE technique to perform flora similarity analysis (cluster analysis) and polymorphism analysis (richness, uniformity, Shannon-Wiener index, Simpson index) and to compare with the GenBank to identify the genus so as to study the variation.

RESULTS: Compared with normal rats, the abundance of Lachnospiraceae, Ruminococcaceae, Lactobacillus intestinalis, Paraprevotella, Lactobacillus murinus, Lactobacillus, Prevotella, Lactobacillus crispatus and Lachnospiracea incertae sedis was significantly reduced and that of Coprobacillus was significantly increased in rats with colorectal cancer. Although the flora diversity between the two groups showed no statistical difference, there was a significant difference in flora composition.

CONCLUSION: The composition of fecal microflora changes in rats with colorectal cancer compared with normal rats, with the number of beneficial bacteria reduced and that of potential pathogens increased.

Dietary probiotic supplementation (Shewanella putrefaciens Pdp11) modulates gut microbiota and promotes growth and condition in Senegalese sole larviculture

Probiotic supplementation in fish aquaculture has significantly increased in the last decade due to its beneficial effect on fish performance. Probiotic use at early stages of fish development may contribute to better face metamorphosis and weaning stress. In the present work, we studied the influence of Shewanella putrefaciens Pdp11 supplementation on growth, body composition and gut microbiota in Senegalese sole (Solea senegalensis) during larval and weaning development. S. putrefaciens Pdp11 was incorporated using Artemia as live vector (2.5 × 10⁷ cfu mL⁻¹) and supplied to sole specimens in a co-feeding regime (10-86 DAH) by triplicate. Probiotic addition promoted early metamorphosis and a significantly higher growth in length at 24 DAH larvae. S. putrefaciens Pdp11 also modulated gut microbiota and significantly increased protein content and DHA/EPA ratios in sole fry (90 DAH). This nutritional enhancement is considered especially important after weaning, where significantly higher growth in length and weight was observed in probiotic fish. Moreover, a less heterogeneous fish size in length was detected since metamorphosis till the end of weaning, being of interest for sole aquaculture production. After weaning, fish showed significantly higher growth (length and weight) and less variable lengths in fish when supplemented with probiotics. Both the enhancement of nutritional condition and the decrease in size variability associated with probiotic addition are highly interesting for sole aquaculture production.

Changes in the composition and diversity of the bacterial microbiota associated with oysters (Crassostrea corteziensis, Crassostrea gigas and Crassostrea sikamea) during commercial production

The resident microbiota of three oyster species (Crassostrea corteziensis, Crassostrea gigas and Crassostrea sikamea) was characterised using a high-throughput sequencing approach (pyrosequencing) that was based on the V3-V5 regions of the 16S rRNA gene. We analysed the changes in the bacterial community beginning with the postlarvae produced in a hatchery, which were later planted at two grow-out cultivation sites until they reached the adult stage. DNA samples from the oysters were amplified, and 31 008 sequences belonging to 13 phyla (including Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes) and 243 genera were generated. Considering all life stages, Proteobacteria was the most abundant phylum, but it showed variations at the genus level between the postlarvae and the adult oysters. Bacteroidetes was the second most common phylum, but it was found in higher abundance in the postlarvae than in adults. The relative abundance showed that the microbiota that was associated with the postlarvae and adults differed substantially, and higher diversity and richness were evident in the postlarvae in comparison with adults of the same species. The site of rearing influenced the bacterial community composition of C. corteziensis and C. sikamea adults. The bacterial groups that were found in these oysters were complex and metabolically versatile, making it difficult to understand the host-bacteria symbiotic relationships; therefore, the physiological and ecological significances of the resident microbiota remain uncertain.

Comparative study of endophytic and endophytic diazotrophic bacterial communities across rice landraces grown in the highlands of northern Thailand

Communities of bacterial endophytes within the rice landraces cultivated in the highlands of northern Thailand were studied using fingerprinting data of 16S rRNA and nifH genes profiling by polymerase chain reaction-denaturing gradient gel electrophoresis. The bacterial communities' richness, diversity index, evenness, and stability were varied depending on the plant tissues, stages of growth, and rice cultivars. These indices for the endophytic diazotrophic bacteria within the landrace rice Bue Wah Bo were significantly the lowest. The endophytic bacteria revealed greater diversity by cluster analysis with seven clusters compared to the endophytic diazotrophic bacteria (three clusters). Principal component analysis suggested that the endophytic bacteria showed that the community structures across the rice landraces had a higher stability than those of the endophytic diazotrophic bacteria. Uncultured bacteria were found dominantly in both bacterial communities, while higher generic varieties were observed in the endophytic diazotrophic bacterial community. These differences in bacterial communities might be influenced either by genetic variation in the rice landraces or the rice cultivation system, where the nitrogen input affects the endophytic diazotrophic bacterial community.

Oral bacterial communities in individuals with type 2 diabetes who live in southern Thailand

Type 2 diabetes mellitus is increasingly common in Thailand and elsewhere. In the present investigation, the bacteriological composition of saliva and supragingival plaque in Thai diabetics with and without active dental caries and in nondiabetics was determined by differential culture and eubacterial DNA profiling. Potential associations between fasting blood sugar and glycosylated hemoglobin (biomarkers of current and historical glucose control, respectively) with decayed, missing, and filled teeth and with salivary Streptococcus and Lactobacillus counts were also investigated. The incidence of active dental caries was greater in the Thai diabetics than in nondiabetics, and the numbers of total streptococci and lactobacilli were significantly higher in supragingival plaque from diabetics than in nondiabetics. Lactobacillus counts in the saliva and supragingival plaque of diabetics with active caries were significantly higher than those in diabetics without active caries. Oral eubacterial DNA profiles of diabetic versus nondiabetic individuals and of diabetics with active caries versus those without active caries could not be readily differentiated through cluster analysis or multidimensional scaling. The elevated caries incidence in the Thai diabetics was positively associated with numbers of bacteria of the acidogenic/acid-tolerant genera Streptococcus and Lactobacillus. Lactobacillus bacterial numbers were further elevated in diabetics with active caries, although salivary eubacterial DNA profiles were not significantly altered.

Identification of dichloroacetic acid degrading Cupriavidus bacteria in a drinking water distribution network model

AIMS

Bacterial community structure and composition of a drinking water network were assessed to better understand this ecosystem in relation to haloacetic acid (HAA) degradation and to identify new bacterial species having HAA degradation capacities.

METHODS AND RESULTS

Biofilm samples were collected from a model system, simulating the end of the drinking water distribution network and supplied with different concentrations of dichloroacetic and trichloroacetic acids at different periods over the course of a year. The samples were analysed by culturing, denaturing gradient gel electrophoresis (DGGE) and sequencing. Pipe diameter and HAA ratios did not impact the bacterial community profiles, but the season had a clear influence. Based on DGGE profiles, it appeared that a particular biomass has developed during the summer compared with the other seasons. Among the bacteria isolated in this study, those from genus Cupriavidus were able to degrade dichloroacetic acid. Moreover, these bacteria degrade dichloroacetic acid at 18°C but not at 10°C.

CONCLUSIONS

The microbial diversity evolved throughout the experiment, but the bacterial community was distinct during the summer. Results obtained on the capacity of Cupriavidus to degrade DCAA only at 18°C but not at 10°C indicate that water temperature is a major element affecting DCAA degradation and confirming observations made regarding season influence on HAA degradation in the drinking water distribution network.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first demonstration of the HAA biodegradation capacity of the genus Cupriavidus.

Microbial contents of vacuum cleaner bag dust and emitted bioaerosols and their implications for human exposure indoors

Vacuum cleaners can release large concentrations of particles, both in their exhaust air and from resuspension of settled dust. However, the size, variability, and microbial diversity of these emissions are unknown, despite evidence to suggest they may contribute to allergic responses and infection transmission indoors. This study aimed to evaluate bioaerosol emission from various vacuum cleaners. We sampled the air in an experimental flow tunnel where vacuum cleaners were run, and their airborne emissions were sampled with closed-face cassettes. Dust samples were also collected from the dust bag. Total bacteria, total archaea, Penicillium/Aspergillus, and total Clostridium cluster 1 were quantified with specific quantitative PCR protocols, and emission rates were calculated. Clostridium botulinum and antibiotic resistance genes were detected in each sample using endpoint PCR. Bacterial diversity was also analyzed using denaturing gradient gel electrophoresis (DGGE), image analysis, and band sequencing. We demonstrated that emission of bacteria and molds (Penicillium/Aspergillus) can reach values as high as 1E5 cell equivalents/min and that those emissions are not related to each other. The bag dust bacterial and mold content was also consistent across the vacuums we assessed, reaching up to 1E7 bacterial or mold cell equivalents/g. Antibiotic resistance genes were detected in several samples. No archaea or C. botulinum was detected in any air samples. Diversity analyses showed that most bacteria are from human sources, in keeping with other recent results. These results highlight the potential capability of vacuum cleaners to disseminate appreciable quantities of molds and human-associated bacteria indoors and their role as a source of exposure to bioaerosols.

Contrasting responses to nutrient enrichment of prokaryotic communities collected from deep sea sites in the southern ocean

Deep water samples (ca. 4,200 m) were taken from two hydrologically-similar sites around the Crozet islands with highly contrasting surface water productivities. Site M5 was characteristic of high productivity waters (high chlorophyll) whilst site M6 was subject to a low productivity regime (low chlorophyll) in the overlying waters. Samples were incubated for three weeks at 4 °C at in-situ and surface pressures, with and without added nutrients. Prokaryotic abundance increased by at least two-fold for all nutrient-supplemented incubations of water from M5 with little difference in abundance between incubations carried out at atmospheric and in-situ pressures. Abundance only increased for incubations of M6 waters (1.6-fold) when they were carried out at in-situ pressures and with added nutrients. Changes in community structure as a result of incubation and enrichment (as measured by DGGE banding profiles and phylogenetic analysis) showed that diversity increased for incubations of M5 waters but decreased for those with M6 waters. Moritella spp. came to dominate incubations carried out under in-situ pressure whilst the Archaeal community was dominated by Crenarchaea in all incubations. Comparisons between atmospheric and in situ pressure incubations demonstrated that community composition was significantly altered and community structure changes in unsuspplemented incubations at in situ pressure was indicative of the loss of functional taxa as a result of depressurisation during sampling. The use of enrichment incubations under in-situ conditions has contributed to understanding the different roles played by microorganisms in deep sea ecosystems in regions of low and high productivity.

Altered colonic function and microbiota profile in a mouse model of chronic depression

BACKGROUND

Depression often coexists with the irritable bowel syndrome (IBS) which is characterized by alterations in gut function. There is emerging evidence that the microbial composition (microbiota) of the gut is altered in IBS, but the basis for this is poorly understood. The aim of this study was to determine whether the induction of chronic depression results in changes in the colonic function and in its microbial community, and to explore underlying mechanisms.

METHODS

Bilateral olfactory bulbectomy (OBx) was used to induce depression-like behavior in mice. Colonic function was assessed by measuring muscle contractility, pellet excretion, c-fos activity, and serotonin levels. Microbiota profiles were obtained using denaturing gradient gel electrophoresis (DGGE). The hypothalamic-pituitary axis (HPA) was assessed by the hypothalamic expression of corticotropin-releasing hormone (CRH). In separate studies, mice without OBx received CRH via intracerebroventricular (ICV) infusion for 4 weeks prior to assessing colonic function and microbiota profiles.

KEY RESULTS

Olfactory bulbectomy mice demonstrated chronic depression- and anxiety-like behaviors associated with elevated central CRH expression and increases in c-Fos activity, serotonin levels, and motility in the colon. These changes were accompanied by an altered intestinal microbial profile. Central CRH administration produced similar changes in behavior and motility and altered the microbiota profile in the colon.

CONCLUSIONS & INFERENCES

The induction of chronic depression alters motor activity and the microbial profile in the colon likely via activation of the HPA. These findings provide a basis for linking the behavioral and gastrointestinal manifestations of IBS.

Comparison of the vaginal microbiota diversity of women with and without human papillomavirus infection: a cross-sectional study

Background

The female genital tract is an important bacterial habitat of the human body, and vaginal microbiota plays a crucial role in vaginal health. The alteration of vaginal microbiota affects millions of women annually, and is associated with numerous adverse health outcomes, including human papillomavirus (HPV) infection. However, previous studies have primarily focused on the association between bacterial vaginosis and HPV infection. Little is known about the composition of vaginal microbial communities involved in HPV acquisition. The present study was performed to investigate whether HPV infection was associated with the diversity and composition of vaginal microbiota.

Methods

A total of 70 healthy women (32 HPV-negative and 38 HPV-positive) with normal cervical cytology were enrolled in this study. Culture-independent polymerase chain reaction-denaturing gradient gel electrophoresis was used to measure the diversity and composition of vaginal microbiota of all subjects.

Results

We found significantly greater biological diversity in the vaginal microbiota of HPV-positive women (p < 0.001). Lactobacillus, including L. gallinarum, L. iners and L. gasseri, was the predominant genus and was detected in all women. No significant difference between HPV-positive and HPV-negative women was found for the frequency of detection of L. gallinarum (p = 0.775) or L. iners (p = 0.717), but L. gasseri was found at a significantly higher frequency in HPV-positive women (p = 0.005). Gardnerella vaginalis was also found at a significantly higher frequency in HPV-positive women (p = 0.031). Dendrograms revealed that vaginal microbiota from the two groups had different profiles.

Conclusions

Our study is the first systematic evaluation of an association between vaginal microbiota and HPV infection, and we have demonstrated that compared with HPV-negative women, the bacterial diversity of HPV-positive women is more complex and the composition of vaginal microbiota is different.