A Bioinformatics Analysis workflow for 16S rRNA Amplicon Sequencing data v1 (protocols.io.bntpmemn)

AbstractMicroorganisms play crucial roles in water recycling, pollution removal and resource recovery in the wastewater industry. The structure of these microbial communities is increasingly understood based on 16S rRNA amplicon sequencing data. However, such data cannot be linked to functional potential in the absence of high-quality metagenome-assembled genomes (MAGs) for nearly all species. Here, we use long-read and short-read sequencing to recover 1083 high-quality MAGs, including 57 closed circular genomes, from 23 Danish full-scale wastewater treatment plants. The MAGs account for ~30% of the community based on relative abundance, and meet the stringent MIMAG high-quality draft requirements including full-length rRNA genes. We use the information provided by these MAGs in combination with >13 years of 16S rRNA amplicon sequencing data, as well as Raman microspectroscopy and fluorescence in situ hybridisation, to uncover abundant undescribed lineages belonging to important functional groups.

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Dramatic differences in gut bacterial densities help to explain the relationship between diet and habitat in rainforest ants

10.1101/114512 ◽

2017 ◽

Cited By ~ 4

Author(s):

Jon G Sanders ◽

Piotr Lukasik ◽

Megan E Frederickson ◽

Jacob A Russell ◽

Ryuichi Koga ◽

...

Keyword(s):

16S Rrna ◽

Microbial Diversity ◽

Tropical Rainforest ◽

Amplicon Sequencing ◽

Sequencing Data ◽

Lowland Tropical Forest ◽

16S Rrna Amplicon Sequencing ◽

Microbial Symbionts ◽

Microbial Symbiosis ◽

Diversity Profiles

AbstractAbundance is a key parameter in microbial ecology, and important to estimates of potential metabolite flux, impacts of dispersal, and sensitivity of samples to technical biases such as laboratory contamination. However, modern amplicon-based sequencing techniques by themselves typically provide no information about the absolute abundance of microbes. Here, we use fluorescence microscopy and quantitative PCR as independent estimates of microbial abundance to test the hypothesis that microbial symbionts have enabled ants to dominate tropical rainforest canopies by facilitating herbivorous diets, and compare these methods to microbial diversity profiles from 16S rRNA amplicon sequencing. Through a systematic survey of ants from a lowland tropical forest, we show that the density of gut microbiota varies across several orders of magnitude among ant lineages, with median individuals from many genera only marginally above detection limits. Supporting the hypothesis that microbial symbiosis is important to dominance in the canopy, we find that the abundance of gut bacteria is positively correlated with stable isotope proxies of herbivory among canopy-dwelling ants, but not among ground-dwelling ants. Notably, these broad findings are much more evident in the quantitative data than in the 16S rRNA sequencing data. Our results help to resolve a longstanding question in tropical rainforest ecology, and have broad implications for the interpretation of sequence-based surveys of microbial diversity.

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Machine Learning-assisted Identification of Bioindicators Predicts Medium-chain Carboxylate Production Performance of an Anaerobic Mixed Culture

10.21203/rs.3.rs-78714/v1 ◽

2020 ◽

Author(s):

Bin Liu ◽

Heike Sträuber ◽

Joao Saraiva ◽

Hauke Harms ◽

Sandra Godinho Silva ◽

...

Keyword(s):

Machine Learning ◽

16S Rrna ◽

Retention Time ◽

Hydraulic Retention Time ◽

Amplicon Sequencing ◽

Production Performance ◽

Chain Elongation ◽

Sequencing Data ◽

Medium Chain ◽

16S Rrna Amplicon Sequencing

Abstract Background: The ability to quantitatively predict ecophysiological functions of microbial communities provides an important step to engineer microbiota for desired functions related to specific biochemical conversions. Here, we present the quantitative prediction of medium-chain carboxylate production in two continuous anaerobic bioreactors from 16S rRNA gene dynamics in enrichment cultures. Results: By progressively shortening the hydraulic retention time from 8 days to 2 days with different temporal schemes in both bioreactors operated for 211 days, we achieved higher productivities and yields of the target products n-caproate and n-caprylate. The datasets generated from each bioreactor were applied independently for training and testing in machine learning. A predictive model was generated by employing the random forest algorithm using 16S rRNA amplicon sequencing data. More than 90% accuracy in the prediction of n-caproate and n-caprylate productivities was achieved. Four inferred bioindicators belonging to the genera Olsenella, Lactobacillus, Syntrophococcus and Clostridium IV suggest their relevance to the higher carboxylate productivity at shorter hydraulic retention time. The recovery of metagenome-assembled genomes of these bioindicators confirmed their genetic potential to perform key steps of medium-chain carboxylate production.Conclusions: Shortening the hydraulic retention time of the continuous bioreactor systems allows to shape the communities with desired chain elongation functions. Using machine-learning, we demonstrated that 16S rRNA amplicon sequencing data can be used to predict bioreactor process performance quantitatively and accurately. Characterising and harnessing bioindicators holds promise to manage reactor microbiota towards selection of the target processes. Our mathematical framework is transferrable to other ecosystem processes and 3 microbial systems where community dynamics is linked to key functions. The general methodology can be adapted to data types of other functional categories such as genes, transcripts, proteins or metabolites.

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NanoRTax, a real-time pipeline for taxonomic and diversity analysis of nanopore 16S rRNA amplicon sequencing data

10.21203/rs.3.rs-938802/v1 ◽

2021 ◽

Author(s):

Héctor Rodriguez-Perez ◽

Laura Ciuffreda ◽

Carlos Flores

Keyword(s):

16S Rrna ◽

Real Time ◽

Amplicon Sequencing ◽

Sequencing Data ◽

Real Time Analysis ◽

16S Rrna Amplicon Sequencing ◽

Oxford Nanopore ◽

Long Read ◽

Cost Efficient ◽

User Friendly

Abstract The study of microbial communities and their applications have been leveraged by the advances in sequencing techniques and bioinformatics tools. The Oxford Nanopore Technologies long read sequencing by nanopores provides a portable and cost-efficient platform for sequencing assays opening the possibility of its application outside specialized environments and real-time analysis of data. To complement the existing efficient library preparation protocol with a streamlined analytic workflow, here we present NanoRTax, a nextflow pipeline for nanopore 16S rRNA amplicon data that features state-of-art taxonomic classification tools and real-time capability. The pipeline is paired with a web-based visual interface to enable user-friendly inspections of the experiment in progress.

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Bacterial Diversity of Breast Milk in Healthy Spanish Women: Evolution from Birth to Five Years Postpartum

Nutrients ◽

10.3390/nu13072414 ◽

2021 ◽

Vol 13 (7) ◽

pp. 2414

Author(s):

Laura Sanjulián ◽

Alexandre Lamas ◽

Rocío Barreiro ◽

Alberto Cepeda ◽

Cristina A. Fente ◽

...

Keyword(s):

Breast Milk ◽

16S Rrna ◽

Human Milk ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Maternal Body Mass Index ◽

16S Rrna Amplicon Sequencing ◽

Spanish Women ◽

Calcium Magnesium ◽

Abundant Genus

The objective of this work was to characterize the microbiota of breast milk in healthy Spanish mothers and to investigate the effects of lactation time on its diversity. A total of ninety-nine human milk samples were collected from healthy Spanish women and were assessed by means of next-generation sequencing of 16S rRNA amplicons and by qPCR. Firmicutes was the most abundant phylum, followed by Bacteroidetes, Actinobacteria, and Proteobacteria. Accordingly, Streptococcus was the most abundant genus. Lactation time showed a strong influence in milk microbiota, positively correlating with Actinobacteria and Bacteroidetes, while Firmicutes was relatively constant over lactation. 16S rRNA amplicon sequencing showed that the highest alpha-diversity was found in samples of prolonged lactation, along with wider differences between individuals. As for milk nutrients, calcium, magnesium, and selenium levels were potentially associated with Streptococcus and Staphylococcus abundance. Additionally, Proteobacteria was positively correlated with docosahexaenoic acid (DHA) levels in breast milk, and Staphylococcus with conjugated linoleic acid. Conversely, Streptococcus and trans-palmitoleic acid showed a negative association. Other factors such as maternal body mass index or diet also showed an influence on the structure of these microbial communities. Overall, human milk in Spanish mothers appeared to be a complex niche shaped by host factors and by its own nutrients, increasing in diversity over time.

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Advantage of 16S rRNA amplicon sequencing in Helicobacter pylori diagnosis

Helicobacter ◽

10.1111/hel.12790 ◽

2021 ◽

Author(s):

Boldbaatar Gantuya ◽

Hashem B. El Serag ◽

Batsaikhan Saruuljavkhlan ◽

Dashdorj Azzaya ◽

Takashi Matsumoto ◽

...

Keyword(s):

Helicobacter Pylori ◽

16S Rrna ◽

Amplicon Sequencing ◽

16S Rrna Amplicon Sequencing

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Lactulose significantly increased the relative abundance of Bifidobacterium and Blautia in mice feces as revealed by 16S rRNA amplicon sequencing

Journal of the Science of Food and Agriculture ◽

10.1002/jsfa.11181 ◽

2021 ◽

Author(s):

Shumao Cui ◽

Jiayu Gu ◽

Xuemei Liu ◽

Dongyao Li ◽

Bingyong Mao ◽

...

Keyword(s):

16S Rrna ◽

Relative Abundance ◽

Amplicon Sequencing ◽

16S Rrna Amplicon Sequencing

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Prokaryotic Communities in the Thalassohaline Tuz Lake, Deep Zone, and Kayacik, Kaldirim and Yavsan Salterns (Turkey) Assessed by 16S rRNA Amplicon Sequencing

Microorganisms ◽

10.3390/microorganisms9071525 ◽

2021 ◽

Vol 9 (7) ◽

pp. 1525

Author(s):

Can Akpolat ◽

Ana Beatriz Fernández ◽

Pinar Caglayan ◽

Baris Calli ◽

Meral Birbir ◽

...

Keyword(s):

16S Rrna ◽

Salt Lake ◽

Amplicon Sequencing ◽

Deep Zone ◽

Biotechnological Potential ◽

16S Rrna Amplicon Sequencing ◽

Physico Chemical ◽

Potential Applications ◽

A Minor ◽

Tuz Lake

Prokaryotic communities and physico-chemical characteristics of 30 brine samples from the thalassohaline Tuz Lake (Salt Lake), Deep Zone, Kayacik, Kaldirim, and Yavsan salterns (Turkey) were analyzed using 16S rRNA amplicon sequencing and standard methods, respectively. Archaea (98.41% of reads) was found to dominate in these habitats in contrast to the domain Bacteria (1.38% of reads). Representatives of the phylum Euryarchaeota were detected as the most predominant, while 59.48% and 1.32% of reads, respectively, were assigned to 18 archaeal genera, 19 bacterial genera, 10 archaeal genera, and one bacterial genus that were determined to be present, with more than 1% sequences in the samples. They were the archaeal genera Haloquadratum, Haloarcula, Halorhabdus, Natronomonas, Halosimplex, Halomicrobium, Halorubrum, Halonotius, Halolamina, Halobacterium, and Salinibacter within the domain Bacteria. The genera Haloquadratum and Halorhabdus were found in all sampling sites. While Haloquadratum, Haloarcula, and Halorhabdus were the most abundant genera, two uncultured Tuz Lake Halobacteria (TLHs) 1 and 2 were detected in high abundance, and an additional uncultured haloarchaeal TLH-3 was found as a minor abundant uncultured taxon. Their future isolation in pure culture would permit us to expand our knowledge on hypersaline thalassohaline habitats, as well as their ecological role and biomedical and biotechnological potential applications.

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16S rRNA Amplicon Sequencing for Metagenomics

Introduction to Bioinformatics in Microbiology - Learning Materials in Biosciences ◽

10.1007/978-3-319-99280-8_8 ◽

2018 ◽

pp. 135-161

Author(s):

Henrik Christensen ◽

Anna Jasmine Andersson ◽

Steffen Lynge Jørgensen ◽

Josef Korbinian Vogt

Keyword(s):

16S Rrna ◽

Amplicon Sequencing ◽

16S Rrna Amplicon Sequencing

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Evaluation of the microbial community structure of potable water samples from occupied and unoccupied buildings using16S rRNA amplicon sequencing

10.1101/2020.07.17.209346 ◽

2020 ◽

Author(s):

Kimothy L Smith ◽

Howard A Shuman ◽

Douglas Findeisen

Keyword(s):

Microbial Community ◽

16S Rrna ◽

Water Samples ◽

Ad Hoc ◽

Microbial Community Composition ◽

Amplicon Sequencing ◽

The Other ◽

Water Usage ◽

16S Rrna Amplicon Sequencing ◽

Oxford Nanopore

AbstractWe conducted two studies of water samples from buildings with normal occupancy and water usage compared to water from buildings that were unoccupied with little or no water usage due to the COVID-19 shutdown. Study 1 had 52 water samples obtained ad hoc from buildings in four metropolitan locations in different states in the US and a range of building types. Study 2 had 36 water samples obtained from two buildings in one metropolitan location with matched water sample types. One of the buildings had been continuously occupied, and the other substantially vacant for approximately 3 months. All water samples were analyzed using 16S rRNA amplicon sequencing with a MinION from Oxford Nanopore Technologies. More than 127 genera of bacteria were identified, including genera with members that are known to include more than 50 putative frank and opportunistic pathogens. While specific results varied among sample locations, 16S rRNA amplicon abundance and the diversity of bacteria were higher in water samples from unoccupied buildings than normally occupied buildings as was the abundance of sequenced amplicons of genera known to include pathogenic bacterial members. In both studies Legionella amplicon abundance was relatively small compared to the abundance of the other bacteria in the samples. Indeed, when present, the relative abundance of Legionella amplicons was lower in samples from unoccupied buildings. Legionella did not predominate in any of the water samples and were found, on average, in 9.6% of samples in Study 1 and 8.3% of samples in Study 2.SynopsisComparison of microbial community composition in the plumbing of occupied and unoccupied buildings during the COVID-19 pandemic shutdown.

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