Integrating high-throughput pyrosequencing and quantitative real-time PCR to analyze complex microbial communities

Full-length 16S rRNA gene sequencing reveals the operating mode and chlorination-aggravated SWRO biofouling at a nuclear power plant

Reverse osmosis (RO) membrane fouling and biological contamination problems faced by seawater desalination systems are microbiologically related. We used full-length 16S rRNA gene sequencing to assess the bacterial community structure and chlorine-resistant bacteria (CRB) associated with biofilm growth in different treatment processes under the winter mode of a chlorinated seawater desalination system in China. At the outset of the winter mode, certain CRB, such as Acinetobacter, Pseudomonas, and Bacillus held sway over the bacterial community structure, playing a pivotal role in biofouling. At the mode's end, Deinococcus and Paracoccus predominated, with Pseudomonas and Roseovarius following suit, while certain CRB genera still maintained their dominance. RO and chlorination are pivotal factors in shaping the bacterial community structure and diversity, and increases in total heterotrophic bacterial counts and community diversity in safety filters may adversely affect the effectiveness of subsequent RO systems. Besides, the bacterial diversity and culturable biomass in the water produced by the RO system remain high, and some conditionally pathogenic CRBs pose a certain microbial risk as a source of drinking water. Targeted removal of these CRBs will be an important area of research for advancing control over membrane clogging and ensuring water quality safety in the future.

AcetoBase Version 2: a database update and re-analysis of formyltetrahydrofolate synthetase amplicon sequencing data from anaerobic digesters

AcetoBase is a public repository and database of formyltetrahydrofolate synthetase (FTHFS) sequences. It is the first systematic collection of bacterial FTHFS nucleotide and protein sequences from genomes and metagenome-assembled genomes and of sequences generated by clone library sequencing. At its publication in 2019, AcetoBase (Version 1) was also the first database to establish connections between the FTHFS gene, the Wood–Ljungdahl pathway and 16S ribosomal RNA genes. Since the publication of AcetoBase, there have been significant improvements in the taxonomy of many bacterial lineages and accessibility/availability of public genomics and metagenomics data. The update to the AcetoBase reference database described here (Version 2) provides new sequence data and taxonomy, along with improvements in web functionality and user interface. The evaluation of this latest update by re-analysis of publicly accessible FTHFS amplicon sequencing data previously analysed with AcetoBase Version 1 revealed significant improvements in the taxonomic assignment of FTHFS sequences.

Database URL: https://acetobase.molbio.slu.se

Bacterial community dynamics and functional variation during the long-term decomposition of cyanobacterial blooms in-vitro

Cyanobacterial blooms drastically influence carbon and nutrient cycling in eutrophic freshwater lakes. To understand the mineralization process of cyanobacteria-derived particulate organic matter (CyanPOM), the aerobic degradation of cyanobacterial blooms dominated by Microcystis sp. was investigated over a 95-day microcosm experiment. Approximately 91%, 95% and 83% of the initial particulate organic carbon (POC), particulate organic nitrogen (PON), and particulate organic phosphorus (POP) were decomposed, respectively. The POC:PON ratio gradually increased from 5.9 to 13.5, whereas the POC:POP ratio gradually decreased from 230.3 to 120. These results indicated that the coupling of POC, PON, and POP changed during the decomposition of CyanPOM. Moreover, approximately 29%, 51% and 46% of POC, PON, and POP were mineralized to dissolved organic carbon, NO₃^-, and PO₄^3-, respectively. Rhodospirillales (10.9%), Burkholderiales (16.5%), and Verrucomicrobiales (14.3%) dominated during the rapid phase (days 0-21), whereas Sphingomonadales (12.8%), Rhizobiales (11.8%), and Xanthomonadales (36.5%) dominated during the slow phase (days 21-50) of CyanPOM decomposition. Nitrospira (16.6%-32.9%) dominated and NO₃^- increased during the refractory phase (days 50-95), thus suggesting the occurrence of nitrification. Redundancy analysis revealed that bacterial communities during rapid decomposition were distinct from those during the slow and refractory periods. POC:POP, NH₄⁺, and NO₃^- were the major driving factors for the patterns of bacterial communities. Furthermore, increase in nitrogen metabolism, methane metabolism, amino acid related enzymes and pyruvate metabolism characterized the functional variation of bacterial communities during degradation. Therefore, CyanPOM is an important nutrient source, and its decomposition level shapes bacterial communities.

Intricacies of assessing the human microbiome in epidemiologic studies

PURPOSE

In the past decade, remarkable relationships have been documented between dysbiosis of the human microbiota and adverse health outcomes. This review seeks to highlight some of the challenges and pitfalls that may be encountered during all stages of microbiota research, from study design and sample collection, to nucleic acid extraction and sequencing, and bioinformatic and statistical analysis.

METHODS

Literature focused on human microbiota research was reviewed and summarized.

RESULTS

Although most studies have focused on surveying the composition of the microbiota, fewer have explored the causal roles of these bacteria, archaea, viruses, and fungi in affecting disease states. Microbiome research is in its relatively early years and many aspects remain challenging, including the complexity and personalized aspects of microbial communities, the influence of exogenous and often confounding factors, the need to apply fundamental principles of ecology and epidemiology, the necessity for new software tools, and the rapidly evolving genomic, technological, and analytical landscapes.

CONCLUSIONS

Incorporating human microbiome research in large epidemiologic studies will soon help us unravel the intricate relationships that we have with our microbial partners and provide interventional opportunities to improve human health.

myPhyloDB: a local web server for the storage and analysis of metagenomic data

myPhyloDB v.1.1.2 is a user-friendly personal database with a browser-interface designed to facilitate the storage, processing, analysis, and distribution of microbial community populations (e.g. 16S metagenomics data). MyPhyloDB archives raw sequencing files, and allows for easy selection of project(s)/sample(s) of any combination from all available data in the database. The data processing capabilities of myPhyloDB are also flexible enough to allow the upload and storage of pre-processed data, or use the built-in Mothur pipeline to automate the processing of raw sequencing data. myPhyloDB provides several analytical (e.g. analysis of covariance,t-tests, linear regression, differential abundance (DESeq2), and principal coordinates analysis (PCoA)) and normalization (rarefaction, DESeq2, and proportion) tools for the comparative analysis of taxonomic abundance, species richness and species diversity for projects of various types (e.g. human-associated, human gut microbiome, air, soil, and water) for any taxonomic level(s) desired. Finally, since myPhyloDB is a local web-server, users can quickly distribute data between colleagues and end-users by simply granting others access to their personal myPhyloDB database. myPhyloDB is available athttp://www.ars.usda.gov/services/software/download.htm?softwareid=472 and more information along with tutorials can be found on our websitehttp://www.myphylodb.org. Database URL:http://www.myphylodb.org.

The Development of a Novel qPCR Assay-Set for Identifying Fecal Contamination Originating from Domestic Fowls and Waterfowl in Israel

The emerging microbial source tracking (MST) methodologies aim to identify fecal contamination originating from domestic and wild animals, and from humans. Avian MST is especially challenging, primarily because the Aves class includes both domesticated and wild species with highly diverse habitats and dietary characteristics. The quest for specific fecal bacterial MST markers can be difficult with respect to attaining sufficient assay sensitivity and specificity. The present study utilizes high throughput sequencing (HTS) to screen bacterial 16S rRNA genes from fecal samples collected from both domestic and wild avian species. Operational taxonomic unit (OTU) analysis was then performed, from which sequences were retained for downstream quantitative polymerase chain reaction (qPCR) marker development. Identification of unique avian host DNA sequences, absent in non-avian hosts, was then carried out using a dedicated database of bacterial 16S rRNA gene taken from the Ribosomal Database Project. Six qPCR assays were developed targeting the 16S rRNA gene of Lactobacillus, Gallibacterium, Firmicutes, Fusobacteriaceae, and other bacteria. Two assays (Av4143 and Av163) identified most of the avian fecal samples and demonstrated sensitivity values of 91 and 70%, respectively. The Av43 assay only identified droppings from battery hens and poultry, whereas each of the other three assays (Av24, Av13, and Av216) identified waterfowl species with lower sensitivities values. The development of an MST assay-panel, which includes both domestic and wild avian species, expands the currently known MST analysis capabilities for decoding fecal contamination.

Molecular characterization of microbial communities in bioaerosols of a coal mine by 454 pyrosequencing and real-time PCR

Microbial diversity and abundance in bioaerosols of a coal mine were analyzed based on 454 pyrosequencing and real-time polymerase chain reaction (PCR). A total of 37,191 high quality sequences were obtained and could be classified into 531, 1730 and 448 operational taxonomic units respectively for archaea, bacteria and fungi at 97% sequence similarity. The Shannon diversity index for archaea, bacteria and fungi was respectively 4.71, 6.29 and 3.86, indicating a high diversity in coal mine bioaerosols. Crenarchaeota, Proteobacteria and Ascomycota were the dominant phyla for archaea, bacteria and fungi, respectively. The concentrations of total archaea, bacteria and fungi were 1.44×10(8), 1.02×10(8) and 9.60×10(4) cells/m3, respectively. Methanotrophs observed in bioaerosols suggested possible methane oxidation in the coal mine. The identified potential pathogens to coal miners, such as Acinetobacter schindleri, Aeromonas cavernicola, Alternaria alternata, Aspergillus penicillioides, Cladosporium cladosporioides, and Penicillium brevicompactum were also observed. This was the first investigation of microbial diversity and abundance in coal mine bioaerosols. The investigation of microbial communities would be favorable in promoting the progress of methane control based on microbial technique and concern on coal miners' health.

Soil moisture and pH control relative contributions of fungi and bacteria to N2O production

Fungal N(2)O production has been progressively recognized, but its controlling factors remain unclear. This study examined the impacts of soil moisture and pH on fungal and bacterial N(2)O production in two ecosystems, conventional farming and plantation forestry. Four treatments, antibiotic-free soil and soil amended with streptomycin, cycloheximide, or both were used to determine N(2)O production of fungi versus bacteria. Soil moisture and pH effects were assessed under 65-90 % water-filled pore space (WFPS) and pH 4.0-9.0, respectively. Irrespective of antibiotic treatments, soil N(2)O fluxes peaked at 85-90 % WFPS and pH 7.0 or 8.0, indicating that both fungi and bacteria preferred more anoxic and neutral or slightly alkaline conditions in producing N(2)O. However, compared with bacteria, fungi contributed more to N(2)O production under sub-anoxic and acidic conditions. Real-time polymerase chain reaction of 16S, ITS rDNA, and denitrifying genes for quantifications of bacteria, fungi, and denitrifying bacteria, respectively, showed that fungi were more abundant at acidic pH, whereas total and denitrifying bacteria favored neutral conditions. Such variations in the abundance appeared to be related to the pH effects on the relative fungal and bacterial contribution to N(2)O production.

Molecular studies neglect apparently gram-negative populations in the human gut microbiota

Studying the relationships between gut microbiota, human health, and diseases is a major challenge that generates contradictory results. Most studies draw conclusions about the gut repertoire using a single biased metagenomics approach. We analyzed 16 different stool samples collected from healthy subjects who were from different areas, had metabolic disorders, were immunocompromised, or were treated with antibiotics at the time of the stool collection. The analyses performed included Gram staining, flow cytometry, transmission electron microscopy (TEM), quantitative real-time PCR (qPCR) of the Bacteroidetes and Firmicutes phyla, and pyrosequencing of the 16S rRNA gene amplicons targeting the V6 region. We quantified 10(10) prokaryotes per gram of feces, which is less than was previously described. The Mann-Whitney test revealed that Gram-negative proportions of the prokaryotes obtained by Gram staining, TEM, and pyrosequencing differed according to the analysis used, with Gram-negative prokaryotes yielding median percentages of 70.6%, 31.0%, and 16.4%, respectively. A comparison of TEM and pyrosequencing analyses highlighted a difference of 14.6% in the identification of Gram-negative prokaryotes, and a Spearman test showed a tendency toward correlation, albeit not significant, in the Gram-negative/Gram-positive prokaryote ratio (ρ = 0.3282, P = 0.2146). In contrast, when comparing the qPCR and pyrosequencing results, a significant correlation was found for the Bacteroidetes/Firmicutes ratio (ρ = 0.6057, P = 0.0130). Our study showed that the entire diversity of the human gut microbiota remains unknown because different techniques generate extremely different results. We found that to assess the overall composition of bacterial communities, multiple techniques must be combined. The biases that exist for each technique may be useful in exploring the major discrepancies in molecular studies.

A fast, highly sensitive double-nested PCR-based method to screen fish immunobiomes

Efficient methods for constructing 16S tag amplicon libraries for pyrosequencing are needed for the rapid and thorough screening of infectious bacterial diversity from host tissue samples. Here we have developed a double-nested PCR methodology that generates 16S tag amplicon libraries from very small amounts of bacteria/host samples. This methodology was tested for 133 kidney samples from the lake whitefish Coregonus clupeaformis (Salmonidae) sampled in five different lake populations. The double-nested PCR efficiency was compared with two other PCR strategies: single primer pair amplification and simple nested PCR. The double-nested PCR was the only amplification strategy to provide highly specific amplification of bacterial DNA. The resulting 16S amplicon libraries were synthesized and pyrosequenced using 454 FLX technology to analyse the variation of pathogenic bacteria abundance. The proportion of the community sequenced was very high (Good's coverage estimator; mean = 95.4%). Furthermore, there were no significant differences of sequence coverage among samples. Finally, the occurrence of chimeric amplicons was very low. Therefore, the double-nested PCR approach provides a rapid, informative and cost-effective method for screening fish immunobiomes and most likely applicable to other low-density microbiomes as well.

BactQuant: an enhanced broad-coverage bacterial quantitative real-time PCR assay

BACKGROUND

Bacterial load quantification is a critical component of bacterial community analysis, but a culture-independent method capable of detecting and quantifying diverse bacteria is needed. Based on our analysis of a diverse collection of 16 S rRNA gene sequences, we designed a broad-coverage quantitative real-time PCR (qPCR) assay--BactQuant--for quantifying 16 S rRNA gene copy number and estimating bacterial load. We further utilized in silico evaluation to complement laboratory-based qPCR characterization to validate BactQuant.

METHODS

The aligned core set of 4,938 16 S rRNA gene sequences in the Greengenes database were analyzed for assay design. Cloned plasmid standards were generated and quantified using a qPCR-based approach. Coverage analysis was performed computationally using >670,000 sequences and further evaluated following the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines.

RESULTS

A bacterial TaqMan® qPCR assay targeting a 466 bp region in V3-V4 was designed. Coverage analysis showed that 91% of the phyla, 96% of the genera, and >80% of the 89,537 species analyzed contained at least one perfect sequence match to the BactQuant assay. Of the 106 bacterial species evaluated, amplification efficiencies ranged from 81 to 120%, with r2-value of >0.99, including species with sequence mismatches. Inter- and intra-run coefficient of variance was <3% and <16% for Ct and copy number, respectively.

CONCLUSIONS

The BactQuant assay offers significantly broader coverage than a previously reported universal bacterial quantification assay BactQuant in vitro performance was better than the in silico predictions.

Molecular-beacon-based tricomponent probe for SNP analysis in folded nucleic acids

Hybridization probes are often inefficient in the analysis of single-stranded DNA or RNA that are folded in stable secondary structures. A molecular beacon (MB) probe is a short DNA hairpin with a fluorophore and a quencher attached to opposite sides of the oligonucleotide. The probe is widely used in real-time analysis of specific DNA and RNA sequences. This study demonstrates how a conventional MB probe can be used for the analysis of nucleic acids that form very stable (T(m) > 80 °C) hairpin structures. Here we demonstrate that the MB probe is not efficient in direct analysis of secondary structure-folded analytes, whereas a MB-based tricomponent probe is suitable for these purposes. The tricomponent probe takes advantage of two oligonucleotide adaptor strands f and m. Each adaptor strand contains a fragment complementary to the analyte and a fragment complementary to a MB probe. In the presence of a specific analyte, the two adaptor strands hybridize to the analyte and the MB probe, thus forming a quadripartite complex. DNA strand f binds to the analyte with high affinity and unwinds its secondary structure. Strand m forms a stable complex only with the fully complementary analyte. The MB probe fluorescently reports the formation of the quadripartite associate. It was demonstrated that the DNA analytes folded in hairpin structures with stems containing 5, 6, 7, 8, 9, 11, or 13 base pairs can be detected in real time with the limit of detection (LOD) lying in the nanomolar range. The stability of the stem region in the DNA analyte did not affect the LOD. Analytes containing single base substitutions in the stem or in the loop positions were discriminated from the fully complementary DNA at room temperature. The tricomponent probe promises to simplify nucleic acid analysis at ambient temperatures in such applications as in vivo RNA monitoring, detection of pathogens, and single nucleotide polymorphism (SNP) genotyping by DNA microarrays.

Effects of solids retention time on methanogenesis in anaerobic digestion of thickened mixed sludge

When a bench-scale digester fed thickened mixed sludge was operated over an SRT range of 4-20 days, removal efficiencies for total chemical oxygen demand and volatile suspended solids declined with decreasing SRT (especially <10 days), but methanogenesis was stable for SRT as low as 5 days. Quantitative PCR analyses showed that methanogens declined steadily for SRT<10 days, with the acetate-cleaving Methanosaetaceae becoming more dominant. Clone-library analyses indicated significant shifts in bacterial population from 20 to 4 day SRT: declining Chloroflexi (28 to 4.5%) and Syntrophomonas (9 to 0%), but increasing Bacteroidetes (12.5 to 20%) and two acetogenic genera belonging to the phyla Firmicutes and Spirochaetales (6.3 to 12%). Thus, the decrease in the apparent hydrolysis constant (khyd-app) with higher SRT and the process limiting size of Methanosaetaceae with the lower SRT are proactive signs for defining rate limitation in anaerobic digestion.