The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

McDonald, Daniel; Clemente, José C.; Kuczynski, Justin; Rideout, Jai Ram; Stombaugh, Jesse; Wendel, Doug; Wilke, Andreas; Huse, Susan M.; Hufnagle, John; Meyer, Patrick; Knight, Rob; Caporaso, J. Gregory

doi:10.1186/2047-217x-1-7

Cited by 718 publications

(525 citation statements)

References 22 publications

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“…Subsequently, samples were rarefied to contain the same number of reads (n ϭ 5,288), and diversity estimates (the Chao1 richness and Shannon-Weaver diversity indices) were calculated. Taxonomy was assigned to the reads, using the LCAClassifier taxonomic classifier (34), by comparison with the sequences in the Greengenes database (version 13_8) (35), and OTU tables were made with the biological observation matrix (BIOM) format (36) and imported into SigmaPlot software (version 12.0; Systat Software, Inc., CA, USA) to make plots and perform statistical analyses on relative OTU abundances. Where possible, OTUs were assigned to the genus level; however, some OTUs could not be determined to a level lower than class, order, or family.…”

Section: Methodsmentioning

confidence: 99%

Establishment of Bacterial Herbicide Degraders in a Rapid Sand Filter for Bioremediation of Phenoxypropionate-Polluted Groundwater

Feld

Nielsen

Hansen

et al. 2016

Appl Environ Microbiol

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In this study, we investigated the establishment of natural bacterial degraders in a sand filter treating groundwater contaminated with the phenoxypropionate herbicides (RS)-2-(4-chloro-2-methylphenoxy)propanoic acid (MCPP) and (RS)-2-(2,4-dichlorophenoxy)propanoic acid (DCPP) and the associated impurity/catabolite 4-chlorophenoxypropanoic acid (4-CPP). A pilot facility was set up in a contaminated landfill site. Anaerobic groundwater was pumped up and passed through an aeration basin and subsequently through a rapid sand filter, which is characterized by a short residence time of the water in the filter. For 3 months, the degradation of DCPP, MCPP, and 4-CPP in the sand filter increased to 15 to 30% of the inlet concentration. A significant selection for natural bacterial herbicide degraders also occurred in the sand filter. Using a most-probable-number (MPN) method, we found a steady increase in the number of culturable phenoxypropionate degraders, reaching approximately 5 ؋ 10 5 degraders per g sand by the end of the study. Using a quantitative PCR targeting the two phenoxypropionate degradation genes, rdpA and sdpA, encoding stereospecific dioxygenases, a parallel increase was observed, but with the gene copy numbers being about 2 to 3 log units higher than the MPN. In general, the sdpA gene was more abundant than the rdpA gene, and the establishment of a significant population of bacteria harboring sdpA occurred faster than the establishment of an rdpA gene-carrying population. The identities of the specific herbicide degraders in the sand filter were assessed by Illumina MiSeq sequencing of 16S rRNA genes from sand filter samples and from selected MPN plate wells. We propose a list of potential degrader bacteria involved in herbicide degradation, including representatives belonging to the Comamonadaceae and Sphingomonadales.G roundwater is a valuable resource that is used for drinking water in many countries all over the world. The quality of the water is vital to our health, and regulations have been made to control the concentration of contaminants and protect the groundwater (1). A major concern is leaching of pesticides mainly from agricultural areas but also from urban areas or from point sources (2). In the European Union, a legal threshold limit has been set at 0.1 g/liter for any given pesticide or 0.5 g/liter for a total concentration of mixed pesticides in drinking water (3).In Denmark, monitoring of the groundwater status has detected pesticides in almost 40% of the investigated wells, and the concentrations exceed the allowed threshold limit in 12% of the wells (4). Phenoxypropionate herbicides, including the compounds (RS)-2-(2,4-dichlorophenoxy)propanoic acid (known as DCPP or dichlorprop) and (RS)-2-(4-chloro-2-methylphenoxy)propanoic acid (known as MCPP or mecoprop), are among the pesticides frequently found in contaminated wells (4). The herbicides are, in particular, a problem in old landfill areas, from where they are leaching into the groundwater as a point source contamination (5). Phe...

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Section: Methodsmentioning

confidence: 99%

Establishment of Bacterial Herbicide Degraders in a Rapid Sand Filter for Bioremediation of Phenoxypropionate-Polluted Groundwater

Feld

Nielsen

Hansen

et al. 2016

Appl Environ Microbiol

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“…All chimera-checked and quality-filtered sequences were clustered into operational taxonomic units (OTUs) at a 97% identity cutoff, and clusters were assigned taxonomic designations using the greengenes database (13_8 97). After clustering and .biom table (93) creation, all singleton, chloroplast, insect, mitochondrial, and unclassified clusters were removed from the data set; these clusters represented sequences that were ϳ0.2% of the total number of sequences in the data set.…”

Section: Methodsmentioning

confidence: 99%

Death Becomes Them: Bacterial Community Dynamics and Stilbene Antibiotic Production in Cadavers of Galleria mellonella Killed by Heterorhabditis and Photorhabdus spp

Wollenberg

Jagdish

Slough

et al. 2016

Appl Environ Microbiol

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Insect larvae killed by entomopathogenic nematodes are thought to contain bacterial communities dominated by a single bacterial genus, that of the nematode's bacterial symbiont. In this study, we used next-generation sequencing to profile bacterial community dynamics in greater wax moth (Galleria mellonella) larvae cadavers killed by Heterorhabditis nematodes and their Photorhabdus symbionts. We found that, although Photorhabdus strains did initially displace an Enterococcus-dominated community present in uninfected G. mellonella insect larvae, the cadaver community was not static. Twelve days postinfection, Photorhabdus shared the cadaver with Stenotrophomonas species. Consistent with this result, Stenotrophomonas strains isolated from infected cadavers were resistant to Photorhabdus-mediated toxicity in solid coculture assays. We isolated and characterized a Photorhabdus-produced antibiotic from G. mellonella cadavers, produced it synthetically, and demonstrated that both the natural and synthetic compounds decreased G. mellonella-associated Enterococcus growth, but not Stenotrophomonas growth, in vitro. Finally, we showed that the Stenotrophomonas strains described here negatively affected Photorhabdus growth in vitro. Our results add an important dimension to a broader understanding of Heterorhabditis-Photorhabdus biology and also demonstrate that interspecific bacterial competition likely characterizes even a theoretically monoxenic environment, such as a Heterorhabditis-Photorhabdus-parasitized insect cadaver. IMPORTANCEUnderstanding, and eventually manipulating, both human and environmental health depends on a complete accounting of the forces that act on and shape microbial communities. One of these underlying forces is hypothesized to be resource competition. A resource that has received little attention in the general microbiological literature, but likely has ecological and evolutionary importance, is dead/decaying multicellular organisms. Metazoan cadavers, including those of insects, are ephemeral and nutrient-rich environments, where resource competition might shape interspecific macrobiotic and microbiotic interactions. This study is the first to use a next-generation sequencing approach to study the community dynamics of bacteria within a model insect cadaver system: insect larvae parasitized by entomopathogenic nematodes and their bacterial symbionts. By integrating bioinformatic, biochemical, and classic in vitro microbiological approaches, we have provided mechanistic insight into how antibiotic-mediated bacterial interactions may shape community dynamics within insect cadavers.

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“…Quality control processing and singleton removal was carried out via the UPARSE pipeline (for example, usearch -fastq_ maxee 0.5, usearch -sortbysize -minsize 2) including de novo and reference-based chimera detection (Edgar, 2013). The resulting operational taxonomic unit (OTU) table was converted to Biological Observation Matrix (BIOM) format (McDonald et al, 2012a). Taxonomy was assigned using the Ribosomal Database Project (RDP) classifier (Wang et al, 2007) against the updated May 2013 '13_5/13_8' Greengenes database (Werner et al, 2011;McDonald et al, 2012b) via the parallel_assign_taxonomy_rdp.py script in QIIME.…”

Section: Amplicon Sequencing and Analysismentioning

confidence: 99%

Contrasting taxonomic stratification of microbial communities in two hypersaline meromictic lakes

et al. 2015

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Hypersaline meromictic lakes are extreme environments in which water stratification is associated with powerful physicochemical gradients and high salt concentrations. Furthermore, their physical stability coupled with vertical water column partitioning makes them important research model systems in microbial niche differentiation and biogeochemical cycling. Here, we compare the prokaryotic assemblages from Ursu and Fara Fund hypersaline meromictic lakes (Transylvanian Basin, Romania) in relation to their limnological factors and infer their role in elemental cycling by matching taxa to known taxon-specific biogeochemical functions. To assess the composition and structure of prokaryotic communities and the environmental factors that structure them, deepcoverage small subunit (SSU) ribosomal RNA (rDNA) amplicon sequencing, community domainspecific quantitative PCR and physicochemical analyses were performed on samples collected along depth profiles. The analyses showed that the lakes harbored multiple and diverse prokaryotic communities whose distribution mirrored the water stratification patterns. Ursu Lake was found to be dominated by Bacteria and to have a greater prokaryotic diversity than Fara Fund Lake that harbored an increased cell density and was populated mostly by Archaea within oxic strata. In spite of their contrasting diversity, the microbial populations indigenous to each lake pointed to similar physiological functions within carbon degradation and sulfate reduction. Furthermore, the taxonomy results coupled with methane detection and its stable C isotope composition indicated the presence of a yet-undescribed methanogenic group in the lakes' hypersaline monimolimnion. In addition, ultrasmall uncultivated archaeal lineages were detected in the chemocline of Fara Fund Lake, where the recently proposed Nanohaloarchaeota phylum was found to thrive.

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The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

Cited by 718 publications

References 22 publications

Establishment of Bacterial Herbicide Degraders in a Rapid Sand Filter for Bioremediation of Phenoxypropionate-Polluted Groundwater

Establishment of Bacterial Herbicide Degraders in a Rapid Sand Filter for Bioremediation of Phenoxypropionate-Polluted Groundwater

Death Becomes Them: Bacterial Community Dynamics and Stilbene Antibiotic Production in Cadavers of Galleria mellonella Killed by Heterorhabditis and Photorhabdus spp

Contrasting taxonomic stratification of microbial communities in two hypersaline meromictic lakes

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