Universal ligation-detection-reaction microarray applied for compost microbes

Food Waste Composting and Microbial Community Structure Profiling

Over the last decade, food waste has been one of the major issues globally as it brings a negative impact on the environment and health. Rotting discharges methane, causing greenhouse effect and adverse health effects due to pathogenic microorganisms or toxic leachates that reach agricultural land and water system. As a solution, composting is implemented to manage and reduce food waste in line with global sustainable development goals (SDGs). This review compiles input on the types of organic composting, its characteristics, physico-chemical properties involved, role of microbes and tools available in determining the microbial community structure. Composting types: vermi-composting, windrow composting, aerated static pile composting and in-vessel composting are discussed. The diversity of microorganisms in each of the three stages in composting is highlighted and the techniques used to determine the microbial community structure during composting such as biochemical identification, polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE), terminal restriction fragment length polymorphism (T-RFLP) and single strand-conformation polymorphism (SSCP), microarray analysis and next-generation sequencing (NGS) are discussed. Overall, a good compost, not only reduces waste issues, but also contributes substantially to the economic and social sectors of a nation.

New species of Talaromyces isolated from maize, indoor air, and other substrates

Talaromyces strains isolated from maize seeds and the built environment were examined taxonomically because they could not be identified as previously described species. Using phenotypic analysis, DNA sequencing, and phylogenetic and concordance analyses, the authors discovered and described 10 new species in sect. Islandici and 1 new species in sect. Subinflati. Taxonomic novelties in sect. Islandici are Talaromyces delawarensis, T. herodensis, T. juglandicola, T. kilbournensis, T. novojersensis, T. ricevillensis, T. rogersiae, T. siglerae, T. subtropicalis, and T. tiftonensis, and the species from sect. Subinflata is T. tzapotlensis. The isolate of T. siglerae is unusual in Talaromyces because it produced a Sagenomella-like anamorph, but phylogenetic analysis placed it in Talaromyces. Talaromyces rotundus is known from a few isolates, but searches with internal transcribed spacer (ITS) sequences in GenBank revealed that it is commonly endolichenous with Lasallia hispanica. Talaromyces wortmannii also has a role as an endophyte of the aquatic plant Persicaria amphibia, based on ITS sequence records from GenBank.

Design and validation of a DNA-microarray for phylogenetic analysis of bacterial communities in different oral samples and dental implants

The quali-quantitative characterization of the oral microbiota is crucial for an exhaustive knowledge of the oral ecology and the modifications of the microbial composition that occur during periodontal pathologies. In this study, we designed and validated a new phylogenetic DNA-microarray (OralArray) to quickly and reliably characterize the most representative bacterial groups that colonize the oral cavity. The OralArray is based on the Ligation Detection Reaction technology associated to Universal Arrays (LDR-UA), and includes 22 probe sets targeted to bacteria belonging to the phyla Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, Fusobacteria, and Spirochaete. The tool is characterized by high specificity, sensitivity and reproducibility. The OralArray was successfully tested and validated on different oral samples (saliva, lingual plaque, supragingival plaque, and healing cap) collected from 10 healthy subjects. For each specimen, a microbial signature was obtained, and our results established the presence of an oral microbial profile specific for each subject. Moreover, the tool was applied to evaluate the efficacy of a disinfectant treatment on the healing caps before their usage. The OralArray is, thus, suitable to study the microbiota associated with various oral sites and to monitor changes arising from therapeutic treatments.

Diversity and dynamics of the DNA- and cDNA-derived compost fungal communities throughout the commercial cultivation process for Agaricus bisporus

Commercial cultivation of the button mushroom Agaricus bisporus is performed through the inoculation of a semipasteurized composted material. Pasteurization of the compost material prior to inoculation results in a substrate with a fungal community that becomes dominated by A. bisporus. However, little is known about the composition and activity in the wider fungal community beyond the presence of A. bisporus in compost throughout the mushroom cropping process. In this study, the fungal cropping compost community was characterized by sequencing nuc rDNA ITS1-5.8S-ITS2 amplified from extractable DNA and RNA. The fungal community generated from DNA extracts identified a diverse community containing 211 unique species, although only 51 were identified from cDNA. Agaricus bisporus was found to dominate in the DNA-derived fungal community for the duration of the cropping process. However, analysis of cDNA extracts found A. bisporus to dominate only up to the first crop flush, after which activity decreased sharply and a much broader fungal community became active. This study has highlighted the diverse fungal community that is present in mushroom compost during cropping.

Development of a microarray-based tool to characterize vaginal bacterial fluctuations and application to a novel antibiotic treatment for bacterial vaginosis

The healthy vaginal microbiota is generally dominated by lactobacilli that confer antimicrobial protection and play a crucial role in health. Bacterial vaginosis (BV) is the most prevalent lower genital tract infection in women in reproductive age and is characterized by a shift in the relative abundances of Lactobacillus spp. to a greater abundance of strictly anaerobic bacteria. In this study, we designed a new phylogenetic microarray-based tool (VaginArray) that includes 17 probe sets specific for the most representative bacterial groups of the human vaginal ecosystem. This tool was implemented using the ligase detection reaction-universal array (LDR-UA) approach. The entire probe set properly recognized the specific targets and showed an overall sensitivity of 6 to 12 ng per probe. The VaginArray was applied to assess the efficacy of rifaximin vaginal tablets for the treatment of BV, analyzing the vaginal bacterial communities of 22 BV-affected women treated with rifaximin vaginal tablets at a dosage of 25 mg/day for 5 days. Our results showed the ability of rifaximin to reduce the growth of various BV-related bacteria (Atopobium vaginae, Prevotella, Megasphaera, Mobiluncus, and Sneathia spp.), with the highest antibiotic susceptibility for A. vaginae and Sneathia spp. Moreover, we observed an increase of Lactobacillus crispatus levels in the subset of women who maintained remission after 1 month of therapy, opening new perspectives for the treatment of BV.

Detection of food spoilage and pathogenic bacteria based on ligation detection reaction coupled to flow-through hybridization on membranes

Traditional culturing methods are still commonly applied for bacterial identification in the food control sector, despite being time and labor intensive. Microarray technologies represent an interesting alternative. However, they require higher costs and technical expertise, making them still inappropriate for microbial routine analysis. The present study describes the development of an efficient method for bacterial identification based on flow-through reverse dot-blot (FT-RDB) hybridization on membranes, coupled to the high specific ligation detection reaction (LDR). First, the methodology was optimized by testing different types of ligase enzymes, labeling, and membranes. Furthermore, specific oligonucleotide probes were designed based on the 16S rRNA gene, using the bioinformatic tool Oligonucleotide Retrieving for Molecular Applications (ORMA). Four probes were selected and synthesized, being specific for Aeromonas spp., Pseudomonas spp., Shewanella spp., and Morganella morganii, respectively. For the validation of the probes, 16 reference strains from type culture collections were tested by LDR and FT-RDB hybridization using universal arrays spotted onto membranes. In conclusion, the described methodology could be applied for the rapid, accurate, and cost-effective identification of bacterial species, exhibiting special relevance in food safety and quality.

Compost: its role, mechanism and impact on reducing soil-borne plant diseases

Soil-borne plant pathogens are responsible for causing many crop plant diseases, resulting in significant economic losses. Compost application to agricultural fields is an excellent natural approach, which can be taken to fight against plant pathogens. The application of organic waste products is also an environmentally friendly alternative to chemical use, which unfortunately is the most common approach in agriculture today. This review analyses pioneering and recent compost research, and also the mechanisms and mode of action of compost microbial communities for reducing the activity of plant pathogens in agricultural crops. In addition, an approach for improving the quality of composts through the microbial communities already present in the compost is presented. Future agricultural practices will almost definitely require integrated research strategies to help combat plant diseases.

Effects of pH and microbial composition on odour in food waste composting

A major problem for composting plants is odour emission. Slow decomposition during prolonged low-pH conditions is a frequent process problem in food waste composting. The aim was to investigate correlations between low pH, odour and microbial composition during food waste composting. Samples from laboratory composting experiments and two large scale composting plants were analysed for odour by olfactometry, as well as physico-chemical and microbial composition. There was large variation in odour, and samples clustered in two groups, one with low odour and high pH (above 6.5), the other with high odour and low pH (below 6.0). The low-odour samples were significantly drier, had lower nitrate and TVOC concentrations and no detectable organic acids. Samples of both groups were dominated by Bacillales or Actinobacteria, organisms which are often indicative of well-functioning composting processes, but the high-odour group DNA sequences were similar to those of anaerobic or facultatively anaerobic species, not to typical thermophilic composting species. High-odour samples also contained Lactobacteria and Clostridia, known to produce odorous substances. A proposed odour reduction strategy is to rapidly overcome the low pH phase, through high initial aeration rates and the use of additives such as recycled compost.

Molecular analysis of meso- and thermophilic microbiota associated with anaerobic biowaste degradation

BACKGROUND

Microbial anaerobic digestion (AD) is used as a waste treatment process to degrade complex organic compounds into methane. The archaeal and bacterial taxa involved in AD are well known, whereas composition of the fungal community in the process has been less studied. The present study aimed to reveal the composition of archaeal, bacterial and fungal communities in response to increasing organic loading in mesophilic and thermophilic AD processes by applying 454 amplicon sequencing technology. Furthermore, a DNA microarray method was evaluated in order to develop a tool for monitoring the microbiological status of AD.

RESULTS

The 454 sequencing showed that the diversity and number of bacterial taxa decreased with increasing organic load, while archaeal i.e. methanogenic taxa remained more constant. The number and diversity of fungal taxa increased during the process and varied less in composition with process temperature than bacterial and archaeal taxa, even though the fungal diversity increased with temperature as well. Evaluation of the microarray using AD sample DNA showed correlation of signal intensities with sequence read numbers of corresponding target groups. The sensitivity of the test was found to be about 1%.

CONCLUSIONS

The fungal community survives in anoxic conditions and grows with increasing organic loading, suggesting that Fungi may contribute to the digestion by metabolising organic nutrients for bacterial and methanogenic groups. The microarray proof of principle tests suggest that the method has the potential for semiquantitative detection of target microbial groups given that comprehensive sequence data is available for probe design.

Detection of human papillomaviruses by polymerase chain reaction and ligation reaction on universal microarray

Sensitive and specific detection of human papillomaviruses (HPV) in cervical samples is a useful tool for the early diagnosis of epithelial neoplasia and anogenital lesions. Recent studies support the feasibility of HPV DNA testing instead of cytology (Pap smear) as a primary test in population screening for cervical cancer. This is likely to be an option in the near future in many countries, and it would increase the efficiency of screening for cervical abnormalities. We present here a microarray test for the detection and typing of 15 most important high-risk HPV types and two low risk types. The method is based on type specific multiplex PCR amplification of the L1 viral genomic region followed by ligation detection reaction where two specific ssDNA probes, one containing a fluorescent label and the other a flanking ZipCode sequence, are joined by enzymatic ligation in the presence of the correct HPV PCR product. Human beta-globin is amplified in the same reaction to control for sample quality and adequacy. The genotyping capacity of our approach was evaluated against Linear Array test using cervical samples collected in transport medium. Altogether 14 out of 15 valid samples (93%) gave concordant results between our test and Linear Array. One sample was HPV56 positive in our test and high-risk positive in Hybrid Capture 2 but remained negative in Linear Array. The preliminary results suggest that our test has accurate multiple HPV genotyping capability with the additional advantages of generic detection format, and potential for high-throughput screening.

Development of a PCR/ligase detection reaction/nanogold-based universal array approach for the detection of low-abundant DNA point mutations

The aim of this study was to investigate the feasibility of combining PCR and ligase detection reaction (LDR) with a novel nano-gold-based universal array for the detection of low abundance point mutations from fetal DNA in maternal plasma samples. The sequence with the target point mutation was first amplified by PCR and then used as a template for LDR in which the upstream specific primer contains a tag sequence at the 5'-end. After hybridization to the probes of a universal array containing anti-tag sequences, the ligated products were bound to streptavidin-labeled nano-gold particles and the hybridization signals were amplified by silver staining. The PCR/LDR/universal array was first tested for sensitivity with nano-gold-based detection, and then this system was applied to detect the low abundance specific mutation IVS2 654(C→T) of the β-globin gene in a model using maternal plasma samples. The nano-gold-based method unambiguously identified a single mutation at a sensitivity of 1:1000. This approach was applied to detect the paternally inherited IVS2 654(C→T) mutation from thirty maternal plasma samples. The results were consistent with those obtained by PCR/reverse dot blot of amniotic fluid cell DNA. The PCR/LDR/nano-gold-based universal array is able to detect low-abundance point mutations with high sensitivity.

Application of phylogenetic microarrays to interrogation of human microbiota

Human-associated microbiota is recognized to play vital roles in maintaining host health, and it is implicated in many disease states. While the initial surge in the profiling of these microbial communities was achieved with Sanger and next-generation sequencing, many oligonucleotide microarrays have also been developed recently for this purpose. Containing probes complementary to small ribosomal subunit RNA gene sequences of community members, such phylogenetic arrays provide direct quantitative comparisons of microbiota composition among samples and between sample groups. Some of the developed microarrays including PhyloChip, Microbiota Array, and HITChip can simultaneously measure the presence and abundance of hundreds and thousands of phylotypes in a single sample. This review describes the currently available phylogenetic microarrays that can be used to analyze human microbiota, delineates the approaches for the optimization of microarray use, and provides examples of recent findings based on microarray interrogation of human-associated microbial communities.

Characterisation of source-separated household waste intended for composting

Large-scale composting of source-separated household waste has expanded in recent years in the Nordic countries. One problem can be low pH at the start of the process. Incoming biowaste at four composting plants was characterised chemically, physically and microbiologically. The pH of food waste ranged from 4.7 to 6.1 and organic acid concentration from 24 to 81 mmol kg(-1). The bacterial diversity in the waste samples was high, with all samples dominated by Gammaproteobacteria, particularly Pseudomonas and Enterobacteria (Escherichia coli, Klebsiella, Enterobacter). Lactic acid bacteria were also numerically important and are known to negatively affect the composting process because the lactic acid they produce lowers the pH, inhibiting other bacteria. The bacterial groups needed for efficient composting, i.e. Bacillales and Actinobacteria, were present in appreciable amounts. The results indicated that start-up problems in the composting process can be prevented by recycling bulk material and compost.

Enhanced discrimination of single nucleotide polymorphisms using 3' nucleotide differences in ligase detection reaction probes

The ligase detection reaction (LDR) is a highly specific genotyping method for single nucleotide variations. Although LDR typically discriminates single nucleotide polymorphism (SNP) alleles at the 3' end of so-called LDR discriminating probes, we designed probes in which the position of nucleotide differences for discrimination was shifted to the second and third nucleotides from the 3' end. Using the 3'-modified probes, we targeted SNPs of the human ABO group and investigated the specificity and efficiency of ligation by a universal LDR assay. We demonstrated that one or two nucleotide shifts of differences in discriminating probes improve the allele balance in detecting both base substitutions and short deletions. In regard to short deletions, moreover, the shifts of nucleotide differences in discriminating probes form the perfect-machted or multiple-mismatched structures (the bulge structures) in the discriminating probe-target DNA duplex and may contribute to enhance ligation efficiency.

Characterization of cultivated fungi isolated from grape marc wastes through the use of amplified rDNA restriction analysis and sequencing

Microbial assessment of grape marc wastes, the residual solid by-product of the wine-industry, was performed by identifying phylogenetically the fungal culturable diversity in order to evaluate environmental and disposal safety issues and to discuss ecological considerations of applications on agricultural land. Fungal spores in grape marc were estimated to 4.7 x 10(6) per g dry weight. Fifty six fungal isolates were classified into eight operational taxonomic units (OTUs) following amplified ribosomal DNA restriction analysis (ARDRA) and colony morphology. Based on 18S rRNA gene and 5.8S rRNA gene-ITS sequencing, the isolates representing OTUs #1, #2, #3, and #4, which comprised 44.6%, 26.8%, 12.5%, and 5.3%, respectively, of the number of the total isolates, were identified as Aspergillus fumigatus, Bionectria ochroleuca, Haematonectria haematococca, and Trichosporon mycotoxinivorans. The isolates of OTU#5 demonstrated high phylogenetic affinity with Penicillium spp., while members of OTUs #6 and #7 were closer linked with Geotrichum candidum var. citri-aurantii and Mycocladus corymbifer, respectively (95.4 and 97.9% similarities in respect to their 5.8S rRNA gene-ITS sequences). The OTU#8 with a single isolate was related with Aspergillus strains. It appears that most of the fungal isolates are associated with the initial raw material. Despite the fact that some of the species identified may potentially act as pathogens, measures such as the avoidance of maintaining large and unprocessed quantities of grape marc wastes in premises without adequate aeration, together with its suitable biological treatment (e.g., composting) prior to any agriculture-related application, could eliminate any pertinent health risks.

High taxonomic level fingerprint of the human intestinal microbiota by ligase detection reaction--universal array approach

Background

Affecting the core functional microbiome, peculiar high level taxonomic unbalances of the human intestinal microbiota have been recently associated with specific diseases, such as obesity, inflammatory bowel diseases, and intestinal inflammation.

Results

In order to specifically monitor microbiota unbalances that impact human physiology, here we develop and validate an original DNA-microarray (HTF-Microbi.Array) for the high taxonomic level fingerprint of the human intestinal microbiota. Based on the Ligase Detection Reaction-Universal Array (LDR-UA) approach, the HTF-Microbi.Array enables specific detection and approximate relative quantification of 16S rRNAs from 30 phylogenetically related groups of the human intestinal microbiota. The HTF-Microbi.Array was used in a pilot study of the faecal microbiota of eight young adults. Cluster analysis revealed the good reproducibility of the high level taxonomic microbiota fingerprint obtained for each of the subject.

Conclusion

The HTF-Microbi.Array is a fast and sensitive tool for the high taxonomic level fingerprint of the human intestinal microbiota in terms of presence/absence of the principal groups. Moreover, analysis of the relative fluorescence intensity for each probe pair of our LDR-UA platform can provide estimation of the relative abundance of the microbial target groups within each samples. Focusing the phylogenetic resolution at division, order and cluster levels, the HTF-Microbi.Array is blind with respect to the inter-individual variability at the species level.

Reduction of odorants in swine manure by carbohydrate and bacterial amendments

Malodors from pig manure storage pits are a problem lacking a cost-efficient solution particularly for small pig (Sus domestica) farms. The objective of this study was to reduce emissions of noxious odorants by changing the conditions in the pig manure to favor an altered microbial community. Sugars (maltose, lactose, and saccharose), carbohydrate-rich waste (maltose syrup and wheat flour), and bacterial amendments (Lactobacillus plantarum and L. amylophilus) were tested for their effect on manure pH, bacterial community, and gaseous emissions. In laboratory experiments, a permanent pH reduction was achieved with all carbohydrates when added to a 5% final concentration. Maltose significantly decreased emissions of sulfur-containing compounds, whereas bacterial amendments had little effect on odorants. Lactobacilli were found in manure receiving carbohydrate amendments alone, but Clostridiales, Bacteroidetes, and Enterobacteriaceae were observed in all treatments (including the control). At the mesocosm (60 L) level, maltose syrup and wheat flour amendments caused clear pH reductions in manure, whereas L. plantarum and L. amylophilus had no additional effect. The addition of maltose syrup and wheat flour to a manure storage pit (600 m(3)) lowered the pH slightly. When the manure was spread onto the fields, the observed reduction in odor was found to be reversible, and the release of malodors was delayed rather than eliminated. We conclude that these methods require further development to produce a reliable technical application.

Application of hybridization control probe to increase accuracy on ligation detection or minisequencing diagnostic microarrays

BACKGROUND

Nucleic acid detection based on ligation reaction or single nucleotide extension of ssDNA probes followed by tag microarray hybridization provides an accurate and sensitive detection tool for various diagnostic purposes. Since microarray quality is crucial for reliable detection, these methods can benefit from correcting for microarray artefacts using specifically adapted techniques.

FINDINGS

Here we demonstrate the application of a per-spot hybridization control oligonucleotide probe and a novel way of computing normalization for tag array data. The method takes into account the absolute value of the detection probe signal and the variability in the control probe signal to significantly alleviate problems caused by artefacts and noise on low quality microarrays.

CONCLUSIONS

Diagnostic microarray platforms require experimental and computational tools to enable efficient correction of array artefacts. The techniques presented here improve the signal to noise ratio and help in determining true positives with better statistical significance and in allowing the use of arrays with poor quality that would otherwise be discarded.