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Background: Most of our knowledge about the remarkable microbial diversity on Earth comes from sequencing the 16S rRNA gene. The use of next-generation sequencing methods has increased sample number and sequencing depth, but the read length of the most widely used sequencing platforms today is quite short, requiring the researcher to choose a subset of the gene to sequence (typically 16-33% of the total length). Thus, many bacteria may share the same amplified region, and the resolution of profiling is inherently limited. Platforms that offer ultra-long read lengths, whole genome shotgun sequencing approaches, and computational frameworks formerly suggested by us and by others all allow different ways to circumvent this problem yet suffer various shortcomings. There is a need for a simple and low-cost 16S rRNA gene-based profiling approach that harnesses the short read length to provide a much larger coverage of the gene to allow for high resolution, even in harsh conditions of low bacterial biomass and fragmented DNA.
Results: This manuscript suggests Short MUltiple Regions Framework (SMURF), a method to combine sequencing results from different PCR-amplified regions to provide one coherent profiling. The de facto amplicon length is the total length of all amplified regions, thus providing much higher resolution compared to current techniques. Computationally, the method solves a convex optimization problem that allows extremely fast reconstruction and requires only moderate memory. We demonstrate the increase in resolution by in silico simulations and by profiling two mock mixtures and real-world biological samples. Reanalyzing a mock mixture from the Human Microbiome Project achieved about twofold improvement in resolution when combing two independent regions. Using a custom set of six primer pairs spanning about 1200 bp (80%) of the 16S rRNA gene, we were able to achieve ~ 100-fold improvement in resolution compared to a single region, over a mock mixture of common human gut bacterial isolates. Finally, the profiling of a Drosophila melanogaster microbiome using the set of six primer pairs provided a ~ 100-fold increase in resolution and thus enabling efficient downstream analysis.
Conclusions: SMURF enables the identification of near full-length 16S rRNA gene sequences in microbial communities, having resolution superior compared to current techniques. It may be applied to standard sample preparation protocols with very little modifications. SMURF also paves the way to high-resolution profiling of low-biomass and fragmented DNA, e.g., in the case of formalin-fixed and paraffin-embedded samples, fossil-derived DNA, or DNA exposed to other degrading conditions. The approach is not restricted to combining amplicons of the 16S rRNA gene and may be applied to any set of amplicons, e.g., in multilocus sequence typing (MLST).
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http://dx.doi.org/10.1186/s40168-017-0396-x | DOI Listing |
Int J Nanomedicine
December 2024
School of Life Science and Medicine, Shandong University of Technology, Zibo, 255000, People's Republic of China.
Purpose: This study aimed to synthesize curcumin-modified selenium (Cur/Se) nanoparticles via a simple and green method for tumour treatment and explore their effects on the gut microbiota.
Methods: Curcumin was applied as a reducing and capping agent for the construction of Cur/Se nanoparticles with Tween 80 as a stabilizer. The drug release behaviour and DPPH and ABTS radical scavenging activities of the Cur/Se nanoparticles were detected.
Heliyon
December 2024
Engineering Research Center of Applied Technology of Pharmacogenomics (Ministry of Education, China), Hunan Key Laboratory of Pharmacomicrobiomics, Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, China.
Recent studies have revealed that intratumoral microbiota is implicated in pancreatic cancer (PC), yet the spectra of intratumoral microbiota and their relationship with PC in Chinese patients remained to be clarified. In this study, tumor and paired paracancerous tissue from 53 patients were profiled by bacterial 16S rRNA gene sequencing. Both and -diversity displayed significant differences between tumors and adjacent tissues, with higher diversity in tumors.
View Article and Find Full Text PDFNPJ Biofilms Microbiomes
December 2024
Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Hannover, Germany.
Biofilm-associated peri-implant infections pose a major problem in modern medicine. The understanding of biofilm development is hampered by biofilm complexity and the lack of robust clinical models. This study comprehensively characterized the dynamics of early biofilm formation in the transmucosal passage of implant abutments in 12 patients.
View Article and Find Full Text PDFAntonie Van Leeuwenhoek
December 2024
Universidad Nacional, Escuela de Ciencias Biológicas, Laboratorio de Análisis Genómico (LAGen), Heredia, 83-3000, Costa Rica.
Live cultures, including Nannochloropsis oculata and Brachionus plicatilis, are essential in aquaculture due to its economic and nutritional value for commercial fish species. Pathogens and probiotics can be introduced to aquaculture systems by live feed, with variations in abundance influenced by environmental physicochemical parameters. To investigate this, amplicon sequencing of the V3-V4 region of the 16S rRNA was conducted using Illumina MiSeq to elucidate bacterial abundances and their variations in response to changes in physicochemical parameters in live feed cultures.
View Article and Find Full Text PDFAntonie Van Leeuwenhoek
December 2024
All-Russian Collection of Microorganisms (VKM), Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, 142290, Russia.
Four salt-tolerant and aromatics degrading strains used in this study were isolated from polluted technogenic soil on the territory of the Verkhnekamsk potash deposit (Russia). The strains were aerobic, Gram-stain-positive, non-motile, non-endospore-forming irregular rods, exhibiting a marked rod-coccus growth cycle. They contained lysine-based peptidoglycan, teichulosonic acid and poly(glycosyl phosphate) polymers in the cell walls.
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