Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples

Environmental Microbiology, Journal Year: 2015, Volume and Issue: 18(5), P. 1403 - 1414

Published: Aug. 14, 2015

Microbial community analysis via high-throughput sequencing of amplified 16S rRNA genes is an essential microbiology tool. We found the popular primer pair 515F (515F-C) and 806R greatly underestimated (e.g. SAR11) or overestimated Gammaproteobacteria) common marine taxa. evaluated samples mock communities (containing 11 27 clones), showing alternative primers 515F-Y (5'-GTGYCAGCMGCCGCGGTAA) 926R (5'-CCGYCAATTYMTTTRAGTTT) yield more accurate estimates abundances, produce longer amplicons that can differentiate taxa unresolvable with 515F-C/806R, amplify eukaryotic 18S rRNA. Mock 515F-Y/926R yielded closer observed composition versus expected (r(2) = 0.95) compared 515F-Y/806R ∼ 0.5). Unexpectedly, biases against SAR11 in field (∼4-10-fold) were stronger than (∼2-fold). Correcting a mismatch to Thaumarchaea 515F-C increased their apparent abundance samples, but not as much using rather 806R. With plankton rich DNA (> 1 μm size fraction), sequences averaged ∼17% all sequences. A single strongly bias amplification, even perfectly matched exhibit preferential amplification. show beyond silico predictions, testing important selection.

Language: Английский

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A communal catalogue reveals Earth’s multiscale microbial diversity

Nature, Journal Year: 2017, Volume and Issue: 551(7681), P. 457 - 463

Published: Oct. 31, 2017

Abstract Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding its fundamental structure. Despite recent advances in DNA sequencing, a lack standardized protocols common analytical frameworks impedes comparisons among studies, hindering development global inferences about life on Earth. Here we present meta-analysis community samples collected by hundreds researchers for Earth Microbiome Project. Coordinated new methods, particularly use exact sequences instead clustered operational taxonomic units, enable bacterial archaeal ribosomal RNA gene to be followed across multiple studies allow us explore patterns at an unprecedented scale. The result is both reference database giving context sequence data framework incorporating from future fostering increasingly complete characterization Earth’s diversity.

Language: Английский

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Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys

mSystems, Journal Year: 2015, Volume and Issue: 1(1)

Published: Dec. 18, 2015

Designing primers for PCR-based taxonomic surveys that amplify a broad range of phylotypes in varied community samples is difficult challenge, and the comparability data sets amplified with requires attention. Here, we examined performance modified 16S rRNA gene internal transcribed spacer (ITS) archaea/bacteria fungi, respectively, nonaquatic samples. We moved primer bar codes to 5' end, allowing different 3' pairings, such as 515f/926r pair, which amplifies variable regions 4 5 gene. additionally demonstrated modifications 515f/806r (variable region 4) improves detection Thaumarchaeota clade SAR11 marine samples, do not degrade on taxa already effectively by original set. Alterations fungal ITS did result differential but overall improved compared primers. In both cases, should be widely adopted amplicon studies. IMPORTANCE continue uncover wealth information connecting microbes important ways human environmental ecology. As our scientific knowledge technical abilities improve, tools used microbiome can improve accuracy techniques, ensuring identify groundbreaking connections between ecosystems they populate, from ice caps body. It confirm these cause new, detrimental biases would inhibit field rather than move it forward. therefore two recently pairs target taxonomically discriminatory bacterial genomic DNA introduce new when variety sample types, soil skin. This confirms utility maintaining currently recommended research techniques state art.

Language: Английский

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Environmental stress destabilizes microbial networks

The ISME Journal, Journal Year: 2021, Volume and Issue: 15(6), P. 1722 - 1734

Published: Jan. 15, 2021

Language: Английский

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Environmental DNA

Oxford University Press eBooks, Journal Year: 2018, Volume and Issue: unknown

Published: Feb. 15, 2018

Abstract Environmental DNA (eDNA), i.e. released in the environment by any living form, represents a formidable opportunity to gather high-throughput and standard information on distribution or feeding habits of species. It has therefore great potential for applications ecology biodiversity management. However, this research field is fast-moving, involves different areas expertise currently lacks approaches, which calls an up-to-date comprehensive synthesis. monitoring covers current methods based eDNA, with particular focus “eDNA metabarcoding”. Intended scientists managers, it provides background allow design sound experiments. revisits all steps necessary produce high-quality metabarcoding data such as sampling, metabarcode design, optimization PCR sequencing protocols, well analysis large datasets. All these are presented discussing challenges eDNA-based approaches infer parameters ecological processes. The last chapters book review how been used so far unravel novel patterns diversity space time, detect species, answer new questions various ecosystems organisms. constitutes essential reading graduate students, researchers practitioners who do not have strong molecular genetics willing use eDNA biomonitoring.

Language: Английский

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American Gut: an Open Platform for Citizen Science Microbiome Research

mSystems, Journal Year: 2018, Volume and Issue: 3(3)

Published: May 14, 2018

Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging integrate extent of microbial molecular diversity in stool remains unknown. Using standardized protocols Earth Microbiome Project sample contributions over 10,000 citizen-scientists, together with an open research network, we compare specimens primarily United States, Kingdom, Australia one another environmental samples. Our results show unexpected range beta-diversity microbiomes compared samples; demonstrate utility procedures for removing effects overgrowth during room-temperature shipping revealing phenotype correlations; uncover new molecules kinds communities metabolome; examine emergent associations among microbiome, metabolome, plants that are consumed (rather than relying on reductive categorical variables such as veganism, which little or no explanatory power). We also living resource cross-cohort comparison confirm existing between psychiatric illness reveal change within individual surgery, providing a paradigm education. IMPORTANCE citizen science, self-selected cohort samples through mail at room temperature recaptures many known clinically collected cohorts reveals ones. Of particular interest is integrating n = 1 study population data, showing after events surgery can exceed differences distinct biomes, effect diverse diet, untargeted metabolomics hundreds

Language: Английский

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SAR11 Bacteria: The Most Abundant Plankton in the Oceans

Annual Review of Marine Science, Journal Year: 2016, Volume and Issue: 9(1), P. 231 - 255

Published: Sept. 30, 2016

SAR11 is a group of small, carbon-oxidizing bacteria that reach global estimated population size 2.4×1028 cells-approximately 25% all plankton. They are found throughout the oceans but their largest numbers in stratified, oligotrophic gyres, which an expanding habitat warming oceans. likely had Precambrian origin and, over geological time, evolved into niche harvesting labile, low-molecular-weight dissolved organic matter (DOM). cells minimal and complexity, phenomenon known as streamlining thought to benefit them by lowering material costs replication maximizing transport functions essential competition at ultralow nutrient concentrations. One surprises metabolism ability both oxidize produce variety volatile compounds can diffuse atmosphere. divide slowly lack many forms regulation commonly used bacterial adjust changing environmental conditions. As result genome reduction, they require unusual range nutrients, leads complex biochemical interactions with other The study providing insight biogeochemistry labile DOM affecting microbiology beyond marine science model for understanding evolution function streamlined cells.

Language: Английский

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Comparing Microbiome Sampling Methods in a Wild Mammal: Fecal and Intestinal Samples Record Different Signals of Host Ecology, Evolution

Frontiers in Microbiology, Journal Year: 2018, Volume and Issue: 9

Published: May 1, 2018

The gut microbiome is a community of host-associated symbiotic microbes that fulfills multiple key roles in host metabolism, immune function, and tissue development. Given the ability to impact fitness, there increasing interest studying wild animals better understand these communities context ecology evolution. Human research protocols are well established, but wildlife still developing field. Currently, no standardized set best practices guiding collection samples from wildlife. Gut microflora typically sampled either by fecal collection, rectal swabbing, or destructively sampling intestinal contents animal. Studies rarely include more than one technique comparison methods currently exists for mammal. Although some studies have hypothesized nested subset microbiome, this hypothesis has not been formally tested system. To address issues, we examined guano (feces) distal mucosa 17 species free-ranging bats Lamanai, Belize, using 16S rRNA amplicon sequencing compare microbial across sample types. We found diversity composition intestine differed substantially. In addition, conclude signatures evolution retained microbiomes based on mucosal samples, samples. Conversely, signal diet These results suggest interchangeable, two microbiotas record different information about which they isolated.

Language: Английский

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Innovations to culturing the uncultured microbial majority

Nature Reviews Microbiology, Journal Year: 2020, Volume and Issue: 19(4), P. 225 - 240

Published: Oct. 22, 2020

Language: Английский

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Microbial abundance, activity and population genomic profiling with mOTUs2

Nature Communications, Journal Year: 2019, Volume and Issue: 10(1)

Published: March 4, 2019

Abstract Metagenomic sequencing has greatly improved our ability to profile the composition of environmental and host-associated microbial communities. However, dependency most methods on reference genomes, which are currently unavailable for a substantial fraction species, introduces estimation biases. We present an updated functionally extended tool based universal (i.e., reference-independent), phylogenetic marker gene (MG)-based operational taxonomic units (mOTUs) enabling profiling >7700 species. As more than 30% them could not previously be quantified at this resolution, relative abundance estimates mOTUs accurate compared other methods. new feature, we show that mOTUs, essential housekeeping genes, demonstrably well-suited quantification basal transcriptional activity community members. Furthermore, single nucleotide variation profiles estimated using reflect those from whole allows comparing strain populations (e.g., across different human body sites).

Language: Английский

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