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  1. Book ; Online: cameronmartino/HS-bacteria-COVID19

    Cameron Martino

    v1.0.0

    2020  

    Abstract: Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 ... ...

    Abstract Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity
    Keywords covid19
    Publishing date 2020-08-05
    Publishing country eu
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Context-aware deconvolution of cell–cell communication with Tensor-cell2cell

    Erick Armingol / Hratch M. Baghdassarian / Cameron Martino / Araceli Perez-Lopez / Caitlin Aamodt / Rob Knight / Nathan E. Lewis

    Nature Communications, Vol 13, Iss 1, Pp 1-

    2022  Volume 15

    Abstract: Cellular contexts such as disease state, organismal life stage and tissue microenvironment, shape intercellular communication, and ultimately affect an organism’s phenotypes. Here, the authors present Tensor-cell2cell, an unsupervised method for ... ...

    Abstract Cellular contexts such as disease state, organismal life stage and tissue microenvironment, shape intercellular communication, and ultimately affect an organism’s phenotypes. Here, the authors present Tensor-cell2cell, an unsupervised method for deciphering context-driven intercellular communication.
    Keywords Science ; Q
    Language English
    Publishing date 2022-06-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Clean room microbiome complexity impacts planetary protection bioburden

    Ryan Hendrickson / Camilla Urbaniak / Jeremiah J. Minich / Heidi S. Aronson / Cameron Martino / Ramunas Stepanauskas / Rob Knight / Kasthuri Venkateswaran

    Microbiome, Vol 9, Iss 1, Pp 1-

    2021  Volume 17

    Abstract: Abstract Background The Spacecraft Assembly Facility (SAF) at the NASA’s Jet Propulsion Laboratory is the primary cleanroom facility used in the construction of some of the planetary protection (PP)-sensitive missions developed by NASA, including the ... ...

    Abstract Abstract Background The Spacecraft Assembly Facility (SAF) at the NASA’s Jet Propulsion Laboratory is the primary cleanroom facility used in the construction of some of the planetary protection (PP)-sensitive missions developed by NASA, including the Mars 2020 Perseverance Rover that launched in July 2020. SAF floor samples (n=98) were collected, over a 6-month period in 2016 prior to the construction of the Mars rover subsystems, to better understand the temporal and spatial distribution of bacterial populations (total, viable, cultivable, and spore) in this unique cleanroom. Results Cleanroom samples were examined for total (living and dead) and viable (living only) microbial populations using molecular approaches and cultured isolates employing the traditional NASA standard spore assay (NSA), which predominantly isolated spores. The 130 NSA isolates were represented by 16 bacterial genera, of which 97% were identified as spore-formers via Sanger sequencing. The most spatially abundant isolate was Bacillus subtilis, and the most temporally abundant spore-former was Virgibacillus panthothenticus. The 16S rRNA gene-targeted amplicon sequencing detected 51 additional genera not found in the NSA method. The amplicon sequencing of the samples treated with propidium monoazide (PMA), which would differentiate between viable and dead organisms, revealed a total of 54 genera: 46 viable non-spore forming genera and 8 viable spore forming genera in these samples. The microbial diversity generated by the amplicon sequencing corresponded to ~86% non-spore-formers and ~14% spore-formers. The most common spatially distributed genera were Sphinigobium, Geobacillus, and Bacillus whereas temporally distributed common genera were Acinetobacter, Geobacilllus, and Bacillus. Single-cell genomics detected 6 genera in the sample analyzed, with the most prominent being Acinetobacter. Conclusion This study clearly established that detecting spores via NSA does not provide a complete assessment for the cleanliness of ...
    Keywords Microbial ecology ; QR100-130
    Subject code 590
    Language English
    Publishing date 2021-12-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. 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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  5. Article ; Online: Temporal Stability of the Ruminal Bacterial Communities in Beef Steers

    Brooke A. Clemmons / Cameron Martino / Liesel G. Schneider / Josh Lefler / Mallory M. Embree / Phillip R. Myer

    Scientific Reports, Vol 9, Iss 1, Pp 1-

    2019  Volume 8

    Abstract: Abstract Nutritional studies involving ruminants have traditionally relied on relatively short transition or wash-out periods between dietary treatments, typically two to four weeks. However, little is known about adequate adaptation periods required to ... ...

    Abstract Abstract Nutritional studies involving ruminants have traditionally relied on relatively short transition or wash-out periods between dietary treatments, typically two to four weeks. However, little is known about adequate adaptation periods required to reach stabilization of the rumen microbiome that could provide more accurate results from nutritional studies in ruminants. This study determined the rumen bacterial communities and rumen environment parameters over ten weeks following transition from a forage-based to concentrate-based diet. Several α-diversity metrics, including observed OTUs and Simpson’s Evenness fluctuated throughout the trial, but were typically either greatest (observed OTUs) or lowest (Simpson’s) at week 5 of the trial contrasted from weeks 1 and 10 (P < 0.05). At week 4, several orders associated with the shift to the final bacterial community composition, including Pasteurellales, Aeromonadales, and Bacteroidales. At week 5, rumen pH was correlated with α-diversity (P = 0.005) and predictive of the rumen microbiome signature at week 10 (R2 = 0.48; P = 0.04). Rumen microbiome stability did not occur until approximately 9 weeks following adaptation to the diet and was associated with changes in specific bacterial populations and rumen environment. The results of this study suggest that adaptation and wash-out periods must be re-evaluated in order to accommodate necessary rumen microbiome acclimation.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2019-07-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: A Novel Sparse Compositional Technique Reveals Microbial Perturbations

    Cameron Martino / James T. Morton / Clarisse A. Marotz / Luke R. Thompson / Anupriya Tripathi / Rob Knight / Karsten Zengler

    mSystems, Vol 4, Iss 1, p e00016-

    2019  Volume 19

    Abstract: By accounting for the sparse compositional nature of microbiome data sets, robust Aitchison PCA can yield high discriminatory power and salient feature ranking between microbial niches. The software to perform this analysis is available under an open- ... ...

    Abstract By accounting for the sparse compositional nature of microbiome data sets, robust Aitchison PCA can yield high discriminatory power and salient feature ranking between microbial niches. The software to perform this analysis is available under an open-source license and can be obtained at https://github.com/biocore/DEICODE; additionally, a QIIME 2 plugin is provided to perform this analysis at https://library.qiime2.org/plugins/q2-deicode.The central aims of many host or environmental microbiome studies are to elucidate factors associated with microbial community compositions and to relate microbial features to outcomes. However, these aims are often complicated by difficulties stemming from high-dimensionality, non-normality, sparsity, and the compositional nature of microbiome data sets. A key tool in microbiome analysis is beta diversity, defined by the distances between microbial samples. Many different distance metrics have been proposed, all with varying discriminatory power on data with differing characteristics. Here, we propose a compositional beta diversity metric rooted in a centered log-ratio transformation and matrix completion called robust Aitchison PCA. We demonstrate the benefits of compositional transformations upstream of beta diversity calculations through simulations. Additionally, we demonstrate improved effect size, classification accuracy, and robustness to sequencing depth over the current methods on several decreased sample subsets of real microbiome data sets. Finally, we highlight the ability of this new beta diversity metric to retain the feature loadings linked to sample ordinations revealing salient intercommunity niche feature importance.
    Keywords compositional ; computational biology ; matrix completion ; microbiome ; metagenomics ; Microbiology ; QR1-502
    Subject code 780
    Language English
    Publishing date 2019-02-01T00:00:00Z
    Publisher American Society for Microbiology
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Early microbial markers of periodontal and cardiometabolic diseases in ORIGINS

    Clarisse Marotz / Rebecca Molinsky / Cameron Martino / Bruno Bohn / Sumith Roy / Michael Rosenbaum / Moïse Desvarieux / Melana Yuzefpolskaya / Bruce J. Paster / David R. Jacobs / Paolo C. Colombo / Panos N. Papapanou / Rob Knight / Ryan T. Demmer

    npj Biofilms and Microbiomes, Vol 8, Iss 1, Pp 1-

    2022  Volume 10

    Abstract: Abstract Periodontitis affects up to 50% of individuals worldwide, and 8.5% are diagnosed with diabetes. The high-comorbidity rate of these diseases may suggest, at least in part, a shared etiology and pathophysiology. Changes in oral microbial ... ...

    Abstract Abstract Periodontitis affects up to 50% of individuals worldwide, and 8.5% are diagnosed with diabetes. The high-comorbidity rate of these diseases may suggest, at least in part, a shared etiology and pathophysiology. Changes in oral microbial communities have been documented in the context of severe periodontitis and diabetes, both independently and together. However, much less is known about the early oral microbial markers of these diseases. We used a subset of the ORIGINS project dataset, which collected detailed periodontal and cardiometabolic information from 787 healthy individuals, to identify early microbial markers of periodontitis and its association with markers of cardiometabolic health. Using state-of-the-art compositional data analysis tools, we identified the log-ratio of Treponema to Corynebacterium bacteria to be a novel Microbial Indicator of Periodontitis (MIP), and found that this MIP correlates with poor periodontal health and cardiometabolic markers early in disease pathogenesis in both subgingival plaque and saliva.
    Keywords Microbial ecology ; QR100-130
    Language English
    Publishing date 2022-04-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Diet and feeding pattern modulate diurnal dynamics of the ileal microbiome and transcriptome

    Ana Carolina Dantas Machado / Steven D. Brown / Amulya Lingaraju / Vignesh Sivaganesh / Cameron Martino / Amandine Chaix / Peng Zhao / Antonio F.M. Pinto / Max W. Chang / R. Alexander Richter / Alan Saghatelian / Alan R. Saltiel / Rob Knight / Satchidananda Panda / Amir Zarrinpar

    Cell Reports, Vol 40, Iss 1, Pp 111008- (2022)

    2022  

    Abstract: Summary: Compositional oscillations of the gut microbiome are essential for normal peripheral circadian rhythms, both of which are disrupted in diet-induced obesity (DIO). Although time-restricted feeding (TRF) maintains circadian synchrony and protects ... ...

    Abstract Summary: Compositional oscillations of the gut microbiome are essential for normal peripheral circadian rhythms, both of which are disrupted in diet-induced obesity (DIO). Although time-restricted feeding (TRF) maintains circadian synchrony and protects against DIO, its impact on the dynamics of the cecal gut microbiome is modest. Thus, other regions of the gut, particularly the ileum, the nexus for incretin and bile acid signaling, may play an important role in entraining peripheral circadian rhythms. We demonstrate the effect of diet and feeding rhythms on the ileal microbiome composition and transcriptome in mice. The dynamic rhythms of ileal microbiome composition and transcriptome are dampened in DIO. TRF partially restores diurnal rhythms of the ileal microbiome and transcriptome, increases GLP-1 release, and alters the ileal bile acid pool and farnesoid X receptor (FXR) signaling, which could explain how TRF exerts its metabolic benefits. Finally, we provide a web resource for exploration of ileal microbiome and transcriptome circadian data.
    Keywords small intestine ; lumen ; 16S ; RNA-seq ; microbiota ; bile acids ; Biology (General) ; QH301-705.5
    Subject code 571
    Language English
    Publishing date 2022-07-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: A Novel Sparse Compositional Technique Reveals Microbial Perturbations

    Cameron Martino / James T. Morton / Clarisse A. Marotz / Luke R. Thompson / Anupriya Tripathi / Rob Knight / Karsten Zengler

    mSystems, Vol 4, Iss

    2019  Volume 1

    Abstract: ABSTRACT The central aims of many host or environmental microbiome studies are to elucidate factors associated with microbial community compositions and to relate microbial features to outcomes. However, these aims are often complicated by difficulties ... ...

    Abstract ABSTRACT The central aims of many host or environmental microbiome studies are to elucidate factors associated with microbial community compositions and to relate microbial features to outcomes. However, these aims are often complicated by difficulties stemming from high-dimensionality, non-normality, sparsity, and the compositional nature of microbiome data sets. A key tool in microbiome analysis is beta diversity, defined by the distances between microbial samples. Many different distance metrics have been proposed, all with varying discriminatory power on data with differing characteristics. Here, we propose a compositional beta diversity metric rooted in a centered log-ratio transformation and matrix completion called robust Aitchison PCA. We demonstrate the benefits of compositional transformations upstream of beta diversity calculations through simulations. Additionally, we demonstrate improved effect size, classification accuracy, and robustness to sequencing depth over the current methods on several decreased sample subsets of real microbiome data sets. Finally, we highlight the ability of this new beta diversity metric to retain the feature loadings linked to sample ordinations revealing salient intercommunity niche feature importance. IMPORTANCE By accounting for the sparse compositional nature of microbiome data sets, robust Aitchison PCA can yield high discriminatory power and salient feature ranking between microbial niches. The software to perform this analysis is available under an open-source license and can be obtained at https://github.com/biocore/DEICODE; additionally, a QIIME 2 plugin is provided to perform this analysis at https://library.qiime2.org/plugins/deicode/.
    Keywords compositional ; computational biology ; matrix completion ; microbiome ; metagenomics ; Microbiology ; QR1-502
    Subject code 780
    Language English
    Publishing date 2019-02-01T00:00:00Z
    Publisher American Society for Microbiology
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection

    Andre Mu / Daniel McDonald / Alan K. Jarmusch / Cameron Martino / Caitriona Brennan / Mackenzie Bryant / Gregory C. Humphrey / Julia Toronczak / Tara Schwartz / Dominic Nguyen / Gail Ackermann / Anthony D’Onofrio / Steffanie A. Strathdee / Robert T. Schooley / Pieter C. Dorrestein / Rob Knight / Saima Aslam

    Microbiome, Vol 9, Iss 1, Pp 1-

    2021  Volume 8

    Abstract: Abstract Background Infectious bacterial diseases exhibiting increasing resistance to antibiotics are a serious global health issue. Bacteriophage therapy is an anti-microbial alternative to treat patients with serious bacterial infections. However, the ... ...

    Abstract Abstract Background Infectious bacterial diseases exhibiting increasing resistance to antibiotics are a serious global health issue. Bacteriophage therapy is an anti-microbial alternative to treat patients with serious bacterial infections. However, the impacts to the host microbiome in response to clinical use of phage therapy are not well understood. Results Our paper demonstrates a largely unchanged microbiota profile during 4 weeks of phage therapy when added to systemic antibiotics in a single patient with Staphylococcus aureus device infection. Metabolomic analyses suggest potential indirect cascading ecological impacts to the host (skin) microbiome. We did not detect genomes of the three phages used to treat the patient in metagenomic samples taken from saliva, stool, and skin; however, phages were detected using endpoint-PCR in patient serum. Conclusion Results from our proof-of-principal study supports the use of bacteriophages as a microbiome-sparing approach to treat bacterial infections. Video abstract
    Keywords Bacteriophages ; Phage therapy ; Microbiome ; Metabolomics ; Staphylococcus aureus ; Microbial ecology ; QR100-130
    Subject code 610
    Language English
    Publishing date 2021-04-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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