CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing – standard operating procedure, version 1.1

Abstract Pharmaceuticals find their way to the aquatic environment via wastewater treatment plants (WWTPs). Biotransformation plays an important role in mitigating environmental risks; however, a mechanistic understanding of involved processes is limited. The aim of this study was to evaluate potential relationships between first-order biotransformation rate constants (kb) of nine pharmaceuticals and initial concentration of the selected compounds, and sampling season of the used activated sludge inocula. Four-day bottle experiments were performed with activated sludge from WWTP Groesbeek (The Netherlands) of two different seasons, summer and winter, spiked with two environmentally relevant concentrations (3 and 30 nM) of pharmaceuticals. Concentrations of the compounds were measured by LC–MS/MS, microbial community composition was assessed by 16S rRNA gene amplicon sequencing, and kb values were calculated. The biodegradable pharmaceuticals were acetaminophen, metformin, metoprolol, terbutaline, and phenazone (ranked from high to low biotransformation rates). Carbamazepine, diatrizoic acid, diclofenac, and fluoxetine were not converted. Summer and winter inocula did not show significant differences in microbial community composition, but resulted in a slightly different kb for some pharmaceuticals. Likely microbial activity was responsible instead of community composition. In the same inoculum, different kb values were measured, depending on initial concentration. In general, biodegradable compounds had a higher kb when the initial concentration was higher. This demonstrates that Michealis-Menten kinetic theory has shortcomings for some pharmaceuticals at low, environmentally relevant concentrations and that the pharmaceutical concentration should be taken into account when measuring the kb in order to reliably predict the fate of pharmaceuticals in the WWTP. Key points • Biotransformation and sorption of pharmaceuticals were assessed in activated sludge. • Higher initial concentrations resulted in higher biotransformation rate constants for biodegradable pharmaceuticals. • Summer and winter inocula produced slightly different biotransformation rate constants although microbial community composition did not significantly change. Graphical abstract

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CloVR-Metagenomics: Functional and taxonomic microbial community characterization from metagenomic whole-genome shotgun (WGS) sequences – standard operating procedure, version 1.0

Nature Precedings ◽

10.1038/npre.2011.5886.3 ◽

2011 ◽

Cited By ~ 1

Author(s):

W. Florian Fricke ◽

James White ◽

Cesar Arze ◽

Malcom Matalka ◽

The CloVR Team ◽

...

Keyword(s):

Microbial Community ◽

Operating Procedure ◽

Standard Operating Procedure ◽

Whole Genome Shotgun ◽

Whole Genome ◽

Standard Operating

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Effects of Actinomycete Secondary Metabolites on Sediment Microbial Communities

Applied and Environmental Microbiology ◽

10.1128/aem.02676-16 ◽

2016 ◽

Vol 83 (4) ◽

Cited By ~ 18

Author(s):

Nastassia V. Patin ◽

Michelle Schorn ◽

Kristen Aguinaldo ◽

Tommie Lincecum ◽

Bradley S. Moore ◽

...

Keyword(s):

Microbial Community ◽

Secondary Metabolites ◽

Microbial Communities ◽

Community Composition ◽

Marine Sediments ◽

Microbial Community Composition ◽

Amplicon Sequencing ◽

Next Generation ◽

Content Type ◽

Predatory Bacteria

ABSTRACT Marine sediments harbor complex microbial communities that remain poorly studied relative to other biomes such as seawater. Moreover, bacteria in these communities produce antibiotics and other bioactive secondary metabolites, yet little is known about how these compounds affect microbial community structure. In this study, we used next-generation amplicon sequencing to assess native microbial community composition in shallow tropical marine sediments. The results revealed complex communities comprised of largely uncultured taxa, with considerable spatial heterogeneity and known antibiotic producers comprising only a small fraction of the total diversity. Organic extracts from cultured strains of the sediment-dwelling actinomycete genus Salinispora were then used in mesocosm studies to address how secondary metabolites shape sediment community composition. We identified predatory bacteria and other taxa that were consistently reduced in the extract-treated mesocosms, suggesting that they may be the targets of allelopathic interactions. We tested related taxa for extract sensitivity and found general agreement with the culture-independent results. Conversely, several taxa were enriched in the extract-treated mesocosms, suggesting that some bacteria benefited from the interactions. The results provide evidence that bacterial secondary metabolites can have complex and significant effects on sediment microbial communities. IMPORTANCE Ocean sediments represent one of Earth's largest and most poorly studied biomes. These habitats are characterized by complex microbial communities where competition for space and nutrients can be intense. This study addressed the hypothesis that secondary metabolites produced by the sediment-inhabiting actinomycete Salinispora arenicola affect community composition and thus mediate interactions among competing microbes. Next-generation amplicon sequencing of mesocosm experiments revealed complex communities that shifted following exposure to S. arenicola extracts. The results reveal that certain predatory bacteria were consistently less abundant following exposure to extracts, suggesting that microbial metabolites mediate competitive interactions. Other taxa increased in relative abundance, suggesting a benefit from the extracts themselves or the resulting changes in the community. This study takes a first step toward assessing the impacts of bacterial metabolites on sediment microbial communities. The results provide insight into how low-abundance organisms may help structure microbial communities in ocean sediments.

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Impact of inter- and intra-individual variation, sample storage and sampling fraction on human stool microbial community profiles

PeerJ ◽

10.7717/peerj.6172 ◽

2019 ◽

Vol 7 ◽

pp. e6172 ◽

Cited By ~ 8

Author(s):

Yun Kit Yeoh ◽

Zigui Chen ◽

Mamie Hui ◽

Martin C.S. Wong ◽

Wendy C.S. Ho ◽

...

Keyword(s):

Microbial Community ◽

Community Composition ◽

Individual Variation ◽

Large Scale ◽

Microbial Community Composition ◽

Amplicon Sequencing ◽

Relative Effect ◽

Individual Variability ◽

Rrna Gene ◽

Sample Collection

Stools are commonly used as proxies for studying human gut microbial communities as sample collection is straightforward, cheap and non-invasive. In large-scale human population surveys, however, sample integrity becomes an issue as it is not logistically feasible for researchers to personally collect stools from every participant. Instead, participants are usually given guidelines on sample packaging and storage, and asked to deliver their stools to a centralised facility. Here, we tested a number of delivery conditions (temperature, duration and addition of preservative medium) and assessed their effects on stool microbial community composition using 16S rRNA gene amplicon sequencing. The largest source of variability in stool community composition was attributable to inter-individual differences regardless of delivery condition. Although the relative effect of delivery condition on community composition was small compared to inter-individual variability (1.6% vs. 60.5%, permutational multivariate analysis of variance [PERMANOVA]) and temporal variation within subjects over 10 weeks (5.2%), shifts in microbial taxa associated with delivery conditions were non-systematic and subject-specific. These findings indicated that it is not possible to model or accurately predict shifts in stool community composition associated with sampling logistics. Based on our findings, we recommend delivery of fresh, preservative-free stool samples to laboratories within 2 hr either at ambient or chilled temperatures to minimise perturbations to microbial community composition. In addition, subsamples from different fractions of the same stool displayed a small (3.3% vs. 72.6% inter-individual variation, PERMANOVA) but significant effect on community composition. Collection of larger sample volumes for homogenisation is recommended.

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On giant shoulders: How a seamount affects the microbial community composition of seawater and sponges

10.5194/bg-2020-15 ◽

2020 ◽

Author(s):

Kathrin Busch ◽

Ulrike Hanz ◽

Furu Mienis ◽

Benjamin Müller ◽

Andre Franke ◽

...

Keyword(s):

Microbial Community ◽

Community Composition ◽

Dissolved Inorganic Carbon ◽

Environmental Gradients ◽

Microbial Community Composition ◽

Geographic Location ◽

Environmental Parameters ◽

Amplicon Sequencing ◽

The Arctic ◽

Rrna Gene

Abstract. Seamounts represent ideal systems to study the influence and interdependency of environmental gradients at a single geographic location. These topographic features represent a prominent habitat for various forms of life, including microbiota and macrobiota, spanning benthic as well as pelagic organisms. While it is known that seamounts are globally abundant structures, it still remains unclear how and to which extend the complexity of the seafloor is intertwined with the local oceanographic mosaic, biogeochemistry and microbiology of a seamount ecosystem. Along these lines, the present study aimed to explore whether and to which extend seamounts can have an imprint on the microbial community composition of seawater and of sessile benthic invertebrates, sponges. For our high-resolution sampling approach of microbial diversity (16S rRNA gene Amplicon sequencing) along with measurements of inorganic nutrients and other biogeochemical parameters, we focused on the Schulz Bank seamount ecosystem, a sponge ground ecosystem which is located on the Arctic Mid-Ocean Ridge. Seawater samples were collected at two sampling depths (mid-water: MW, and near-bed water: BW) from a total of 19 sampling sites. With a clustering approach we defined microbial micro-habitats within the pelagic realm at Schulz Bank, which were mapped onto the seamount's topography, and related to various environmental parameters (such as suspended particulate matter (SPM), dissolved inorganic carbon (DIC), silicate (SiO4−), phosphate (PO43−), ammonia (NH4+), nitrate (NO32−), nitrite (NO2

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On the robustness of inference of association with the gut microbiota in stool, swab and mucosal tissue samples

10.1101/2021.02.04.429844 ◽

2021 ◽

Author(s):

Shan Sun ◽

Xiangzhu Zhu ◽

Xiang Huang ◽

Harvey J. Murff ◽

Reid M. Ness ◽

...

Keyword(s):

Microbial Community ◽

Gut Microbiota ◽

Community Composition ◽

Microbial Community Composition ◽

Amplicon Sequencing ◽

Taxonomic Composition ◽

Mucosal Tissue ◽

Tissue Samples ◽

16S Rrna Amplicon Sequencing ◽

Functional Profiles

AbstractThe gut microbiota plays an important role in human health and disease. Stool, swab and mucosal tissue samples have been used in individual studies to survey the microbial community but the consequences of using these different sample types are not completely understood. We previously reported differences in microbial community composition with 16S rRNA amplicon sequencing between stool, swab and mucosal tissue samples. Here, we extended the previous study to a larger cohort and performed shotgun metagenome sequencing of 1,397 stool, swab and mucosal tissue samples from 240 participants. Consistent with previous results, taxonomic composition of stool and swab samples was distinct, but still more similar to each other than mucosal tissue samples, which had a substantially different community composition, characterized by a high relative abundance of the mucus metabolizers Bacteroides and Subdoligranulum, as well as bacteria with higher tolerance for oxidative stress such as Escherichia. As has been previously reported, functional profiles were more uniform across sample types than taxonomic profiles with differences between stool and swab samples smaller, but mucosal tissue samples remained distinct from the other two types. When the taxonomic and functional profiles of different sample types were used for inference in association with host phenotypes of age, sex, body mass index (BMI), antibiotics or non-steroidal anti-inflammatory drugs (NSAIDs) use, hypothesis testing using either stool or swab gave broadly similar results, but inference performed on mucosal tissue samples gave results that were generally less consistent with either stool or swab. Our study represents an important resource for the experimental design of studies aimed to understand microbiota perturbations specific to defined micro niches within the human intestinal tract.

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