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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: Taxonomic signatures of cause-specific mortality risk in human gut microbiome

    Aaro Salosensaari / Ville Laitinen / Aki S. Havulinna / Guillaume Meric / Susan Cheng / Markus Perola / Liisa Valsta / Georg Alfthan / Michael Inouye / Jeramie D. Watrous / Tao Long / Rodolfo A. Salido / Karenina Sanders / Caitriona Brennan / Gregory C. Humphrey / Jon G. Sanders / Mohit Jain / Pekka Jousilahti / Veikko Salomaa /
    Rob Knight / Leo Lahti / Teemu Niiranen

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Volume 8

    Abstract: Gut microbiome composition has a role in health and disease. Here the authors show that microbiome signatures related to the Enterobacteriaceae family are associated with cause-specific mortality risk in a well phenotyped Finish population over a 15-year ...

    Abstract Gut microbiome composition has a role in health and disease. Here the authors show that microbiome signatures related to the Enterobacteriaceae family are associated with cause-specific mortality risk in a well phenotyped Finish population over a 15-year follow-up.
    Keywords Science ; Q
    Language English
    Publishing date 2021-05-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. 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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  4. 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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  5. 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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  6. Article ; Online: Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads

    Jon G. Sanders / Sergey Nurk / Rodolfo A. Salido / Jeremiah Minich / Zhenjiang Z. Xu / Qiyun Zhu / Cameron Martino / Marcus Fedarko / Timothy D. Arthur / Feng Chen / Brigid S. Boland / Greg C. Humphrey / Caitriona Brennan / Karenina Sanders / James Gaffney / Kristen Jepsen / Mahdieh Khosroheidari / Cliff Green / Marlon Liyanage /
    Jason W. Dang / Vanessa V. Phelan / Robert A. Quinn / Anton Bankevich / John T. Chang / Tariq M. Rana / Douglas J. Conrad / William J. Sandborn / Larry Smarr / Pieter C. Dorrestein / Pavel A. Pevzner / Rob Knight

    Genome Biology, Vol 20, Iss 1, Pp 1-

    2019  Volume 14

    Abstract: Abstract As metagenomic studies move to increasing numbers of samples, communities like the human gut may benefit more from the assembly of abundant microbes in many samples, rather than the exhaustive assembly of fewer samples. We term this approach ... ...

    Abstract Abstract As metagenomic studies move to increasing numbers of samples, communities like the human gut may benefit more from the assembly of abundant microbes in many samples, rather than the exhaustive assembly of fewer samples. We term this approach leaderboard metagenome sequencing. To explore protocol optimization for leaderboard metagenomics in real samples, we introduce a benchmark of library prep and sequencing using internal references generated by synthetic long-read technology, allowing us to evaluate high-throughput library preparation methods against gold-standard reference genomes derived from the samples themselves. We introduce a low-cost protocol for high-throughput library preparation and sequencing.
    Keywords Leaderboard metagenome ; Long reads ; Benchmark ; Assembly ; Binning ; Biology (General) ; QH301-705.5 ; Genetics ; QH426-470
    Language English
    Publishing date 2019-10-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment

    Clarisse Marotz / Pedro Belda-Ferre / Farhana Ali / Promi Das / Shi Huang / Kalen Cantrell / Lingjing Jiang / Cameron Martino / Rachel E. Diner / Gibraan Rahman / Daniel McDonald / George Armstrong / Sho Kodera / Sonya Donato / Gertrude Ecklu-Mensah / Neil Gottel / Mariana C. Salas Garcia / Leslie Y. Chiang / Rodolfo A. Salido /
    Justin P. Shaffer / Mac Kenzie Bryant / Karenina Sanders / Greg Humphrey / Gail Ackermann / Niina Haiminen / Kristen L. Beck / Ho-Cheol Kim / Anna Paola Carrieri / Laxmi Parida / Yoshiki Vázquez-Baeza / Francesca J. Torriani / Rob Knight / Jack Gilbert / Daniel A. Sweeney / Sarah M. Allard

    Microbiome, Vol 9, Iss 1, Pp 1-

    2021  Volume 15

    Abstract: Abstract Background SARS-CoV-2 is an RNA virus responsible for the coronavirus disease 2019 (COVID-19) pandemic. Viruses exist in complex microbial environments, and recent studies have revealed both synergistic and antagonistic effects of specific ... ...

    Abstract Abstract Background SARS-CoV-2 is an RNA virus responsible for the coronavirus disease 2019 (COVID-19) pandemic. Viruses exist in complex microbial environments, and recent studies have revealed both synergistic and antagonistic effects of specific bacterial taxa on viral prevalence and infectivity. We set out to test whether specific bacterial communities predict SARS-CoV-2 occurrence in a hospital setting. Methods We collected 972 samples from hospitalized patients with COVID-19, their health care providers, and hospital surfaces before, during, and after admission. We screened for SARS-CoV-2 using RT-qPCR, characterized microbial communities using 16S rRNA gene amplicon sequencing, and used these bacterial profiles to classify SARS-CoV-2 RNA detection with a random forest model. Results Sixteen percent of surfaces from COVID-19 patient rooms had detectable SARS-CoV-2 RNA, although infectivity was not assessed. The highest prevalence was in floor samples next to patient beds (39%) and directly outside their rooms (29%). Although bed rail samples more closely resembled the patient microbiome compared to floor samples, SARS-CoV-2 RNA was detected less often in bed rail samples (11%). SARS-CoV-2 positive samples had higher bacterial phylogenetic diversity in both human and surface samples and higher biomass in floor samples. 16S microbial community profiles enabled high classifier accuracy for SARS-CoV-2 status in not only nares, but also forehead, stool, and floor samples. Across these distinct microbial profiles, a single amplicon sequence variant from the genus Rothia strongly predicted SARS-CoV-2 presence across sample types, with greater prevalence in positive surface and human samples, even when compared to samples from patients in other intensive care units prior to the COVID-19 pandemic. Conclusions These results contextualize the vast diversity of microbial niches where SARS-CoV-2 RNA is detected and identify specific bacterial taxa that associate with the viral RNA prevalence both in the host and ...
    Keywords Built environment ; SARS-CoV-2 ; 16S rRNA ; Microbiome ; COVID-19 ; Microbial ecology ; QR100-130
    Subject code 500
    Language English
    Publishing date 2021-06-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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