Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research

Comeau, A.; Douglas, Gavin M.; Langille, Morgan G. I.

doi:10.1128/msystems.00127-16

Cited by 508 publications

(402 citation statements)

References 40 publications

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“…To amplify microeukaryotic DNA, we submitted DNA samples for library preparation and sequencing to the IMR facility at Dalhousie University. Library preparation was carried out using the protocol described by Comeau, Li, Tremblay, Carmack, and Lovejoy (), Comeau, Douglas, and Langille () to amplify the V4 region of the 18S rRNA gene with primers E572F: 5′‐CYGCGGTAATTCCAGCTC‐3′ and E1009R: 5′‐AYGGTATCTRATCRTCTTYG‐3′. Paired‐end sequencing was carried out using the Illumina MiSeq (2 × 300 bp) platform.…”

Section: Methodsmentioning

confidence: 99%

Alternate life history phases of a common seaweed have distinct microbial surface communities

et al. 2018

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Macroalgal life histories are complex, often involving the alternation of distinct free-living life history phases that differ in morphology, longevity and ploidy. The surfaces of marine macroalgae support diverse microbial biofilms, yet the degree of microbial variation between alternate phases is unknown. We quantified bacterial (16S rRNA gene) and microeukaryote (18S rRNA gene) communities on the surface of the common intertidal seaweed, Mastocarpus spp., which alternates between gametophyte (foliose, haploid) and sporophyte (encrusting, diploid) life history phases. A large portion (97%) of bacterial taxa on the surface Mastocarpus was also present in samples from the environment, indicating that macroalgal surface communities are largely assembled from the surrounding seawater. Still, changes in the relative abundance of bacterial taxa result in significantly different communities on alternate Mastocarpus life history phases, rocky substrate and seawater at all intertidal elevations. For microeukaryote assemblages, only high intertidal samples had significant differences between life history phases although sporophytes were not different from the rocky substrate at this elevation; gametophytes and sporophytes did not differ in microeukaryote communities in the mid and low zones. By sequencing three host genes, we identified three cryptic species of Mastocarpus in our data set, which co-occur in the mid-to-low intertidal zone. In these samples, M. alaskensis sporophytes harboured distinct bacterial communities compared to M. agardhii and M. intermedius sporophytes, which were not distinguishable. Conversely, microeukaryote communities did not differ among species.

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Section: Methodsmentioning

confidence: 99%

Alternate life history phases of a common seaweed have distinct microbial surface communities

et al. 2018

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“…DNA was amplified using previously described primers targeting the V4-V5 variable region of the 16S rRNA gene of bacteria and archaea, and the V4 region of the 18S rRNA gene of Eukaryotes, respectively (Comeau et al, 2011;Parada et al, 2016;Walters et al, 2016). Tag sequencing of DNA amplicons was carried out on an Illumina MiSeq instrument using 2 × 300 bp paired-end v3 chemistry at the Integrated Microbiome Resource, Dalhousie University (Comeau et al, 2017). Additional sequencing of whole community metagenomes was carried out at selected depths using the Illumina Nextera XT kit as described by the manufacturer.…”

Section: Nucleic Acid Extraction and Sequencingmentioning

confidence: 99%

“…Small subunit rRNA gene sequence processing and analysis. 16S/18S rRNA gene sequences were processed using a QIIME-1 (Caporaso et al, 2010) based workflow (Comeau et al, 2017;. This included merging of paired-end sequences using PEAR (Zhang et al, 2014), discarding sequences <400 bp or with quality <30 over 90% of bases, as well as removing chimera by VSEARCH (Rognes et al, 2016).…”

Section: Processing Of Nucleic Acid Reads and Bioinformatic Analysesmentioning

confidence: 99%

“…Using sortmerna (Kopylova et al, 2012) for reference picking and sumaclust (Mercier et al, 2013) for de novo picking, OTUs (defined by 97% sequence similarity) were picked and clustered against the Greengenes (16S rRNA) and PR 2 (18S rRNA) reference databases (DeSantis et al, 2006;Guillou et al, 2013). Subsequently, low-confidence OTUs (<0.1%) were removed (Comeau et al, 2017). 16S rRNA amplicon reads were rarefied to 6614 reads, which allowed to keep all samples and did not cause perceivable differences in outcome compared to higher thresholds.…”

Section: Processing Of Nucleic Acid Reads and Bioinformatic Analysesmentioning

confidence: 99%

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Geomicrobiology of the carbon, nitrogen and sulphur cycles in Powell Lake: a permanently stratified water column containing ancient seawater

Haas

Desai

LaRoche

et al. 2019

Environmental Microbiology

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Summary We present the first geomicrobiological characterization of the meromictic water column of Powell Lake (British Columbia, Canada), a former fjord, which has been stably stratified since the last glacial period. Its deepest layers (300–350 m) retain isolated, relict seawater from that period. Fine‐scale vertical profiling of the water chemistry and microbial communities allowed subdivision of the water column into distinct geomicrobiological zones. These zones were further characterized by phylogenetic and functional marker genes from amplicon and shotgun metagenome sequencing. Binning of metagenomic reads allowed the linkage of function to specific taxonomic groups. Statistical analyses (analysis of similarities, Bray–Curtis similarity) confirmed that the microbial community structure followed closely the geochemical zonation. Yet, our characterization of the genetic potential relevant to carbon, nitrogen and sulphur cycling of each zone revealed unexpected features, including potential for facultative anaerobic methylotrophy, nitrogen fixation despite high ammonium concentrations and potential micro‐aerobic nitrifiers within the chemocline. At the oxic–suboxic interface, facultative anaerobic potential was found in the widespread freshwater lineage acI (Actinobacteria), suggesting intriguing ecophysiological similarities to the marine SAR11. Evolutionary divergent lineages among diverse phyla were identified in the ancient seawater zone and may indicate novel adaptations to this unusual environment.

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“…High-throughput 16S rRNA gene sequencing Bacterial communities were sequenced by Illumina MiSeq 2 × 300 bp paired-end sequencing of the V6-V8 region of the 16S rRNA gene, amplified using universal bacterial primers B969F and B1406R (Comeau et al 2011(Comeau et al , 2017, at the Integrated Microbiome Resource of the Centre for Comparative Genomics and Evolutionary Bioinformatics (Dalhousie University, Halifax, Nova Scotia, Canada).…”

Section: Identification Of Sponge Specimensmentioning

confidence: 99%

Microbiomes of the Arctic carnivorous sponges Chondrocladia grandis and Cladorhiza oxeata suggest a specific, but differential involvement of bacterial associates

Verhoeven

Dufour

2018

Arctic Science

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While sponges are generally known to host a wide range of microbial associates, the composition and specificity of the microbial communities in carnivorous sponges are poorly understood. We used 16S rRNA gene data to examine and compare the bacterial communities associated with distinct anatomical regions of two carnivorous sponge species, Chondrocladia grandis and Cladorhiza oxeata, sampled from Baffin Bay and the Gulf of Maine (C. grandis only). The two sponge species hosted distinct bacterial communities, with taxonomic diversity being greater in C. grandis. Some bacterial taxa (including particular oligotypes) were consistently recovered in multiple host individuals from geographically distant sites, suggesting specificity. Within C. grandis, certain bacterial taxa were enriched in particular anatomical regions, suggesting functional roles in carnivorous sponge metabolism or other biological processes. Stable isotope analysis provided no evidence for methanotrophy in the sponges examined, but Gulf of Maine C. grandis might incorporate 13 C-depleted carbon via the bacteria-mediated heterotrophic degradation of other hydrocarbons. Overall, our results demonstrate that the carnivorous sponge microbiome appears host species specific and stable, even over large geographical areas. The observed differences in bacterial community composition and diversity between C. grandis and C. oxeata may reflect differences in trophic adaptability, specialization, and overall reliance on associated bacteria.Key words: microbiome, Baffin Island, carnivorous sponges, Chondrocladia grandis, Cladorhiza oxeata.Résumé : Bien qu'il soit reconnu que les éponges accueillent une vaste gamme d'alliés microbiens, la composition et la spécificité des communautés microbiennes chez les éponges carnivores sont mal comprises. Nous avons utilisé des données de gène de 16S rRNA afin d'examiner et de comparer les communautés bactériennes liées aux régions anatomiques distinctes de deux espèces d'éponge carnivore, Chondrocladia grandis et Cladorhiza oxeata, échantillonnées de la baie de Baffin et du golfe du Maine (C. grandis seulement). Les deux espèces d'éponge contiennent des communautés bactériennes distinctes, la diversité taxonomique étant plus grande chez C. grandis. Certains taxons bactériens (incluant des oligotypes particuliers) ont été systématiquement retrouvés chez de multiples individus hôtes provenant de sites géographiquement éloignés, suggérant la spécificité. Chez C. grandis, certains taxons bactériens ont été enrichis dans des régions anatomiques distinctes, suggérant des rôles fonctionnels dans le métabolisme de l'éponge carnivore ou d'autres processus biologiques. L'analyse des isotopes stables n'a fourni aucune preuve de méthanotrophie chez les For personal use only.éponges examinées, mais C. grandis du golfe du Maine pourrait incorporer le carbone appauvri en 13 C via la dégradation hétérotrophe d'autres hydrocarbures par l'intermédiaire de bactéries. En général, nos résultats démontrent que le microbiome d'éponge c...

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Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research

Cited by 508 publications

References 40 publications

Alternate life history phases of a common seaweed have distinct microbial surface communities

Alternate life history phases of a common seaweed have distinct microbial surface communities

Geomicrobiology of the carbon, nitrogen and sulphur cycles in Powell Lake: a permanently stratified water column containing ancient seawater

Microbiomes of the Arctic carnivorous sponges Chondrocladia grandis and Cladorhiza oxeata suggest a specific, but differential involvement of bacterial associates

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