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  1. Article ; Online: A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities

    Justin P Shaffer / Carolina S Carpenter / Cameron Martino / Rodolfo A Salido / Jeremiah J Minich / MacKenzie Bryant / Karenina Sanders / Tara Schwartz / Gregory Humphrey / Austin D Swafford / Rob Knight

    BioTechniques (2022)

    2022  

    Abstract: Microbial communities contain a broad phylogenetic diversity of organisms; however, the majority of methods center on describing bacteria and archaea. Fungi are important symbionts in many ecosystems and are potentially important members of the human ... ...

    Abstract Microbial communities contain a broad phylogenetic diversity of organisms; however, the majority of methods center on describing bacteria and archaea. Fungi are important symbionts in many ecosystems and are potentially important members of the human microbiome, beyond those that can cause disease. To expand our analysis of microbial communities to include data from the fungal internal transcribed spacer (ITS) region, five candidate DNA extraction kits were compared against our standardized protocol for describing bacteria and archaea using 16S rRNA gene amplicon- and shotgun metagenomics sequencing. The results are presented considering a diverse panel of host-associated and environmental sample types and comparing the cost, processing time, well-to-well contamination, DNA yield, limit of detection and microbial community composition among protocols. Across all criteria, the MagMAX Microbiome kit was found to perform best. The PowerSoil Pro kit performed comparably but with increased cost per sample and overall processing time. The Zymo MagBead, NucleoMag Food and Norgen Stool kits were included.
    Keywords Earth Microbiome Project (EMP) ; high-throughput sequencing ; Katharoseq ; Macherey-Nagel ; MagAttract PowerSoil ; mock community ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2022-06-01T00:00:00Z
    Publisher Future Science Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities

    Justin P Shaffer / Clarisse Marotz / Pedro Belda-Ferre / Cameron Martino / Stephen Wandro / Mehrbod Estaki / Rodolfo A Salido / Carolina S Carpenter / Livia S Zaramela / Jeremiah J Minich / MacKenzie Bryant / Karenina Sanders / Serena Fraraccio / Gail Ackermann / Gregory Humphrey / Austin D Swafford / Sandrine Miller-Montgomery / Rob Knight

    BioTechniques, Vol 70, Iss 3, Pp 149-

    2021  Volume 159

    Abstract: One goal of microbial ecology researchers is to capture the maximum amount of information from all organisms in a sample. The recent COVID-19 pandemic, caused by the RNA virus SARS-CoV-2, has highlighted a gap in traditional DNA-based protocols, ... ...

    Abstract One goal of microbial ecology researchers is to capture the maximum amount of information from all organisms in a sample. The recent COVID-19 pandemic, caused by the RNA virus SARS-CoV-2, has highlighted a gap in traditional DNA-based protocols, including the high-throughput methods the authors previously established as field standards. To enable simultaneous SARS-CoV-2 and microbial community profiling, the authors compared the relative performance of two total nucleic acid extraction protocols with the authors' previously benchmarked protocol. The authors included a diverse panel of environmental and host-associated sample types, including body sites commonly swabbed for COVID-19 testing. Here the authors present results comparing the cost, processing time, DNA and RNA yield, microbial community composition, limit of detection and well-to-well contamination between these protocols.
    Keywords 16S rRNA ; DNA extraction ; high-throughput sequencing ; limit of detection ; microbial community ; microbiome ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2021-03-01T00:00:00Z
    Publisher Future Science Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria

    Tiago Leão / Mingxun Wang / Nathan Moss / Ricardo da Silva / Jon Sanders / Sergey Nurk / Alexey Gurevich / Gregory Humphrey / Raphael Reher / Qiyun Zhu / Pedro Belda-Ferre / Evgenia Glukhov / Syrena Whitner / Kelsey L. Alexander / Robert Rex / Pavel Pevzner / Pieter C. Dorrestein / Rob Knight / Nuno Bandeira /
    William H. Gerwick / Lena Gerwick

    Marine Drugs, Vol 19, Iss 20, p

    2021  Volume 20

    Abstract: Microbial natural products are important for the understanding of microbial interactions, chemical defense and communication, and have also served as an inspirational source for numerous pharmaceutical drugs. Tropical marine cyanobacteria have been ... ...

    Abstract Microbial natural products are important for the understanding of microbial interactions, chemical defense and communication, and have also served as an inspirational source for numerous pharmaceutical drugs. Tropical marine cyanobacteria have been highlighted as a great source of new natural products, however, few reports have appeared wherein a multi-omics approach has been used to study their natural products potential (i.e., reports are often focused on an individual natural product and its biosynthesis). This study focuses on describing the natural product genetic potential as well as the expressed natural product molecules in benthic tropical cyanobacteria. We collected from several sites around the world and sequenced the genomes of 24 tropical filamentous marine cyanobacteria. The informatics program antiSMASH was used to annotate the major classes of gene clusters. BiG-SCAPE phylum-wide analysis revealed the most promising strains for natural product discovery among these cyanobacteria. LCMS/MS-based metabolomics highlighted the most abundant molecules and molecular classes among 10 of these marine cyanobacterial samples. We observed that despite many genes encoding for peptidic natural products, peptides were not as abundant as lipids and lipopeptides in the chemical extracts. Our results highlight a number of highly interesting biosynthetic gene clusters for genome mining among these cyanobacterial samples.
    Keywords genomics ; metabolomics ; marine cyanobacteria ; natural products ; biosynthetic potential ; Biology (General) ; QH301-705.5
    Subject code 540
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Exposure to toxic metals triggers unique responses from the rat gut microbiota

    Joshua B. Richardson / Blair C. R. Dancy / Cassandra L. Horton / Young S. Lee / Michael S. Madejczyk / Zhenjiang Zech Xu / Gail Ackermann / Gregory Humphrey / Gustavo Palacios / Rob Knight / John A. Lewis

    Scientific Reports, Vol 8, Iss 1, Pp 1-

    2018  Volume 12

    Abstract: Abstract Our understanding of the interaction between the gut microbiota and host health has recently improved dramatically. However, the effects of toxic metal exposure on the gut microbiota remain poorly characterized. As this microbiota creates a ... ...

    Abstract Abstract Our understanding of the interaction between the gut microbiota and host health has recently improved dramatically. However, the effects of toxic metal exposure on the gut microbiota remain poorly characterized. As this microbiota creates a critical interface between the external environment and the host’s cells, it may play an important role in host outcomes during exposure. We therefore used 16S ribosomal RNA (rRNA) gene sequencing to track changes in the gut microbiota composition of rats exposed to heavy metals. Rats were exposed daily for five days to arsenic, cadmium, cobalt, chromium, nickel, or a vehicle control. Significant changes to microbiota composition were observed in response to high doses of chromium and cobalt, and significant dose-dependent changes were observed in response to arsenic, cadmium and nickel. Many of these perturbations were not uniform across metals. However, bacteria with higher numbers of iron-importing gene orthologs were overly represented after exposure to arsenic and nickel, suggesting some possibility of a shared response. These findings support the utility of the microbiota as a pre-clinical tool for identifying exposures to specific heavy metals. It is also clear that characterizing changes to the functional capabilities of microbiota is critical to understanding responses to metal exposure.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2018-04-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: The genetic basis for adaptation of model-designed syntrophic co-cultures.

    Colton J Lloyd / Zachary A King / Troy E Sandberg / Ying Hefner / Connor A Olson / Patrick V Phaneuf / Edward J O'Brien / Jon G Sanders / Rodolfo A Salido / Karenina Sanders / Caitriona Brennan / Gregory Humphrey / Rob Knight / Adam M Feist

    PLoS Computational Biology, Vol 15, Iss 3, p e

    2019  Volume 1006213

    Abstract: Understanding the fundamental characteristics of microbial communities could have far reaching implications for human health and applied biotechnology. Despite this, much is still unknown regarding the genetic basis and evolutionary strategies underlying ...

    Abstract Understanding the fundamental characteristics of microbial communities could have far reaching implications for human health and applied biotechnology. Despite this, much is still unknown regarding the genetic basis and evolutionary strategies underlying the formation of viable synthetic communities. By pairing auxotrophic mutants in co-culture, it has been demonstrated that viable nascent E. coli communities can be established where the mutant strains are metabolically coupled. A novel algorithm, OptAux, was constructed to design 61 unique multi-knockout E. coli auxotrophic strains that require significant metabolite uptake to grow. These predicted knockouts included a diverse set of novel non-specific auxotrophs that result from inhibition of major biosynthetic subsystems. Three OptAux predicted non-specific auxotrophic strains-with diverse metabolic deficiencies-were co-cultured with an L-histidine auxotroph and optimized via adaptive laboratory evolution (ALE). Time-course sequencing revealed the genetic changes employed by each strain to achieve higher community growth rates and provided insight into mechanisms for adapting to the syntrophic niche. A community model of metabolism and gene expression was utilized to predict the relative community composition and fundamental characteristics of the evolved communities. This work presents new insight into the genetic strategies underlying viable nascent community formation and a cutting-edge computational method to elucidate metabolic changes that empower the creation of cooperative communities.
    Keywords Biology (General) ; QH301-705.5
    Subject code 570
    Language English
    Publishing date 2019-03-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome

    Robert A. Quinn / Sandeep Adem / Robert H. Mills / William Comstock / Lindsay DeRight Goldasich / Gregory Humphrey / Alexander A. Aksenov / Alexei V. Melnik / Ricardo da Silva / Gail Ackermann / Nuno Bandeira / David J. Gonzalez / Doug Conrad / Anthony J. O’Donoghue / Rob Knight / Pieter C. Dorrestein

    Microbiome, Vol 7, Iss 1, Pp 1-

    2019  Volume 13

    Abstract: Abstract Background Studies of the cystic fibrosis (CF) lung microbiome have consistently shown that lung function decline is associated with decreased microbial diversity due to the dominance of opportunistic pathogens. However, how this phenomenon is ... ...

    Abstract Abstract Background Studies of the cystic fibrosis (CF) lung microbiome have consistently shown that lung function decline is associated with decreased microbial diversity due to the dominance of opportunistic pathogens. However, how this phenomenon is reflected in the metabolites and chemical environment of lung secretions remains poorly understood. Methods Here we investigated the microbial and molecular composition of CF sputum samples using 16S rRNA gene amplicon sequencing and untargeted tandem mass spectrometry to determine their interrelationships and associations with clinical measures of disease severity. Results The CF metabolome was found to exist in two states: one from patients with more severe disease that had higher molecular diversity and more Pseudomonas aeruginosa and the other from patients with better lung function having lower metabolite diversity and fewer pathogenic bacteria. The two molecular states were differentiated by the abundance and diversity of peptides and amino acids. Patients with severe disease and more pathogenic bacteria had higher levels of peptides. Analysis of the carboxyl terminal residues of these peptides indicated that neutrophil elastase and cathepsin G were responsible for their generation, and accordingly, these patients had higher levels of proteolytic activity from these enzymes in their sputum. The CF pathogen Pseudomonas aeruginosa was correlated with the abundance of amino acids and is known to primarily feed on them in the lung. Conclusions In cases of severe CF lung disease, proteolysis by host enzymes creates an amino acid-rich environment that P. aeruginosa comes to dominate, which may contribute to the pathogen’s persistence by providing its preferred carbon source.
    Keywords Microbial ecology ; QR100-130
    Subject code 610
    Language English
    Publishing date 2019-02-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: The impact of skin care products on skin chemistry and microbiome dynamics

    Amina Bouslimani / Ricardo da Silva / Tomasz Kosciolek / Stefan Janssen / Chris Callewaert / Amnon Amir / Kathleen Dorrestein / Alexey V. Melnik / Livia S. Zaramela / Ji-Nu Kim / Gregory Humphrey / Tara Schwartz / Karenina Sanders / Caitriona Brennan / Tal Luzzatto-Knaan / Gail Ackermann / Daniel McDonald / Karsten Zengler / Rob Knight /
    Pieter C. Dorrestein

    BMC Biology, Vol 17, Iss 1, Pp 1-

    2019  Volume 20

    Abstract: Abstract Background Use of skin personal care products on a regular basis is nearly ubiquitous, but their effects on molecular and microbial diversity of the skin are unknown. We evaluated the impact of four beauty products (a facial lotion, a ... ...

    Abstract Abstract Background Use of skin personal care products on a regular basis is nearly ubiquitous, but their effects on molecular and microbial diversity of the skin are unknown. We evaluated the impact of four beauty products (a facial lotion, a moisturizer, a foot powder, and a deodorant) on 11 volunteers over 9 weeks. Results Mass spectrometry and 16S rRNA inventories of the skin revealed decreases in chemical as well as in bacterial and archaeal diversity on halting deodorant use. Specific compounds from beauty products used before the study remain detectable with half-lives of 0.5–1.9 weeks. The deodorant and foot powder increased molecular, bacterial, and archaeal diversity, while arm and face lotions had little effect on bacterial and archaeal but increased chemical diversity. Personal care product effects last for weeks and produce highly individualized responses, including alterations in steroid and pheromone levels and in bacterial and archaeal ecosystem structure and dynamics. Conclusions These findings may lead to next-generation precision beauty products and therapies for skin disorders.
    Keywords Skin ; Skin care products ; Mass spectrometry ; Metabolomics ; 16S rRNA sequencing ; Bacteria ; Biology (General) ; QH301-705.5
    Subject code 571
    Language English
    Publishing date 2019-06-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Cohabiting family members share microbiota with one another and with their dogs

    Se Jin Song / Christian Lauber / Elizabeth K Costello / Catherine A Lozupone / Gregory Humphrey / Donna Berg-Lyons / J Gregory Caporaso / Dan Knights / Jose C Clemente / Sara Nakielny / Jeffrey I Gordon / Noah Fierer / Rob Knight

    eLife, Vol

    2013  Volume 2

    Abstract: Human-associated microbial communities vary across individuals: possible contributing factors include (genetic) relatedness, diet, and age. However, our surroundings, including individuals with whom we interact, also likely shape our microbial ... ...

    Abstract Human-associated microbial communities vary across individuals: possible contributing factors include (genetic) relatedness, diet, and age. However, our surroundings, including individuals with whom we interact, also likely shape our microbial communities. To quantify this microbial exchange, we surveyed fecal, oral, and skin microbiota from 60 families (spousal units with children, dogs, both, or neither). Household members, particularly couples, shared more of their microbiota than individuals from different households, with stronger effects of co-habitation on skin than oral or fecal microbiota. Dog ownership significantly increased the shared skin microbiota in cohabiting adults, and dog-owning adults shared more ‘skin’ microbiota with their own dogs than with other dogs. Although the degree to which these shared microbes have a true niche on the human body, vs transient detection after direct contact, is unknown, these results suggest that direct and frequent contact with our cohabitants may significantly shape the composition of our microbial communities.
    Keywords metagenomics ; microbial community transmission ; environmental microbial reservoir ; family structure ; companion animal ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2013-04-01T00:00:00Z
    Publisher eLife Sciences Publications Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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