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264 results on '"Langille, Morgan G. I."'

1. A primer and discussion on DNA-based microbiome data and related bioinformatics analyses

Author

Douglas, Gavin M. and Langille, Morgan G. I.

Subjects
Archaeology, CC1-960, Science
Abstract

The past decade has seen an eruption of interest in profiling microbiomes through DNA sequencing. The resulting investigations have revealed myriad insights and attracted an influx of researchers to the research area. Many newcomers are in need of primers on the fundamentals of microbiome sequencing data types and the methods used to analyze them. Accordingly, here we aim to provide a detailed, but accessible, introduction to these topics. We first present the background on marker-gene and shotgun metagenomics sequencing and then discuss unique characteristics of microbiome data in general. We highlight several important caveats resulting from these characteristics that should be appreciated when analyzing these data. We then introduce the many-faceted concept of microbial functions and several controversies in this area. One controversy in particular is regarding whether metagenome prediction methods (i.e., based on marker-gene sequences) are sufficiently accurate to ensure reliable biological inferences. We next highlight several underappreciated developments regarding the integration of taxonomic and functional data types. This is a highly pertinent topic because although these data types are inherently connected, they are often analyzed independently and primarily only linked anecdotally in the literature. We close by providing our perspective on this topic in addition to the issue of reproducibility in microbiome research, which are both crucial data analysis challenges facing microbiome researchers.

Published
2021
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4. Cross-study analyses of microbial abundance using generalized common factor methods

Author

Hayes, Molly G., Langille, Morgan G. I., and Gu, Hong

Subjects
Statistics - Applications, 62P10
Abstract

By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. Next-generation high-throughput sequencing has led to a new frontier in microbial ecology, promising the ability to leverage the microbiome to make crucial advancements in the environmental and biomedical sciences. However, this is challenging, as genomic data are high-dimensional, sparse, and noisy. Much of this noise reflects the exact conditions under which sequencing took place, and is so significant that it limits consensus-based validation of study results. We propose an ensemble approach for cross-study exploratory analyses of microbial abundance data in which we first estimate the variance-covariance matrix of the underlying abundances from each dataset on the log scale assuming Poisson sampling, and subsequently model these covariances jointly so as to find a shared low-dimensional subspace of the feature space. By viewing the projection of the latent true abundances onto this common structure, the variation is pared down to that which is shared among all datasets, and is likely to reflect more generalizable biological signal than can be inferred from individual datasets. We investigate several ways of achieving this, and demonstrate that they work well on simulated and real metagenomic data in terms of signal retention and interpretability.

Published
2023

10. Nitrogen fixation in the widely distributed marine γ-proteobacterial diazotroph Candidatus Thalassolituus haligoni

Author

Rose, Sonja A., Robicheau, Brent M., Tolman, Jennifer, Fonseca-Batista, Debany, Rowland, Elden, Desai, Dhwani, Ratten, Jenni-Marie, Kantor, Ella Joy H., Comeau, Andre M., Langille, Morgan G. I., Jerlström-Hultqvist, Jon, Devred, Emmanuel, Sarthou, Geraldine, Bertrand, Erin M., LaRoche, Julie, Rose, Sonja A., Robicheau, Brent M., Tolman, Jennifer, Fonseca-Batista, Debany, Rowland, Elden, Desai, Dhwani, Ratten, Jenni-Marie, Kantor, Ella Joy H., Comeau, Andre M., Langille, Morgan G. I., Jerlström-Hultqvist, Jon, Devred, Emmanuel, Sarthou, Geraldine, Bertrand, Erin M., and LaRoche, Julie

Abstract

The high diversity and global distribution of heterotrophic bacterial diazotrophs (HBDs) in the ocean has recently become apparent. However, understanding the role these largely uncultured microorganisms play in marine N-2 fixation poses a challenge due to their undefined growth requirements and the complex regulation of the nitrogenase enzyme. We isolated and characterized Candidatus Thalassolituus haligoni, a member of a widely distributed clade of HBD belonging to the Oceanospirillales. Analysis of its nifH gene via amplicon sequencing revealed the extensive distribution of Cand. T. haligoni across the Pacific, Atlantic, and Arctic Oceans. Pangenome analysis indicates that the isolate shares >99% identity with an uncultured metagenome-assembled genome called Arc-Gamma-03, recently recovered from the Arctic Ocean. Through combined genomic, proteomic, and physiological approaches, we confirmed that the isolate fixes N-2 gas. However, the mechanisms governing nitrogenase regulation in Cand. T. haligoni remain unclear. We propose Cand. T. haligoni as a globally distributed, cultured HBD model species within this understudied clade of Oceanospirillales.

Published
2024
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16. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Author

Bolyen, Evan, Rideout, Jai Ram, Dillon, Matthew R., Bokulich, Nicholas A., Abnet, Christian C., Al-Ghalith, Gabriel A., Alexander, Harriet, Alm, Eric J., Arumugam, Manimozhiyan, Asnicar, Francesco, Bai, Yang, Bisanz, Jordan E., Bittinger, Kyle, Brejnrod, Asker, Brislawn, Colin J., Brown, C. Titus, Callahan, Benjamin J., Caraballo-Rodríguez, Andrés Mauricio, Chase, John, Cope, Emily K., Da Silva, Ricardo, Diener, Christian, Dorrestein, Pieter C., Douglas, Gavin M., Durall, Daniel M., Duvallet, Claire, Edwardson, Christian F., Ernst, Madeleine, Estaki, Mehrbod, Fouquier, Jennifer, Gauglitz, Julia M., Gibbons, Sean M., Gibson, Deanna L., Gonzalez, Antonio, Gorlick, Kestrel, Guo, Jiarong, Hillmann, Benjamin, Holmes, Susan, Holste, Hannes, Huttenhower, Curtis, Huttley, Gavin A., Janssen, Stefan, Jarmusch, Alan K., Jiang, Lingjing, Kaehler, Benjamin D., Kang, Kyo Bin, Keefe, Christopher R., Keim, Paul, Kelley, Scott T., Knights, Dan, Koester, Irina, Kosciolek, Tomasz, Kreps, Jorden, Langille, Morgan G. I., Lee, Joslynn, Ley, Ruth, Liu, Yong-Xin, Loftfield, Erikka, Lozupone, Catherine, Maher, Massoud, Marotz, Clarisse, Martin, Bryan D., McDonald, Daniel, McIver, Lauren J., Melnik, Alexey V., Metcalf, Jessica L., Morgan, Sydney C., Morton, Jamie T., Naimey, Ahmad Turan, Navas-Molina, Jose A., Nothias, Louis Felix, Orchanian, Stephanie B., Pearson, Talima, Peoples, Samuel L., Petras, Daniel, Preuss, Mary Lai, Pruesse, Elmar, Rasmussen, Lasse Buur, Rivers, Adam, Robeson, II, Michael S., Rosenthal, Patrick, Segata, Nicola, Shaffer, Michael, Shiffer, Arron, Sinha, Rashmi, Song, Se Jin, Spear, John R., Swafford, Austin D., Thompson, Luke R., Torres, Pedro J., Trinh, Pauline, Tripathi, Anupriya, Turnbaugh, Peter J., Ul-Hasan, Sabah, van der Hooft, Justin J. J., Vargas, Fernando, Vázquez-Baeza, Yoshiki, Vogtmann, Emily, von Hippel, Max, Walters, William, Wan, Yunhu, Wang, Mingxun, Warren, Jonathan, Weber, Kyle C., Williamson, Charles H. D., Willis, Amy D., Xu, Zhenjiang Zech, Zaneveld, Jesse R., Zhang, Yilong, Zhu, Qiyun, Knight, Rob, and Caporaso, J. Gregory

Published
2019
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18. Enhancement of the gut barrier integrity by a microbial metabolite through the Nrf2 pathway

Author

Singh, Rajbir, Chandrashekharappa, Sandeep, Bodduluri, Sobha R., Baby, Becca V., Hegde, Bindu, Kotla, Niranjan G., Hiwale, Ankita A., Saiyed, Taslimarif, Patel, Paresh, Vijay-Kumar, Matam, Langille, Morgan G. I., Douglas, Gavin M., Cheng, Xi, Rouchka, Eric C., Waigel, Sabine J., Dryden, Gerald W., Alatassi, Houda, Zhang, Huang-Ge, Haribabu, Bodduluri, Vemula, Praveen K., and Jala, Venkatakrishna R.

Published
2019
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30. Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Author

Bolyen, Evan, Rideout, Jai Ram, Dillon, Matthew R., Bokulich, Nicholas A., Abnet, Christian C., Al-Ghalith, Gabriel A., Alexander, Harriet, Alm, Eric J., Arumugam, Manimozhiyan, Asnicar, Francesco, Bai, Yang, Bisanz, Jordan E., Bittinger, Kyle, Brejnrod, Asker, Brislawn, Colin J., Brown, C. Titus, Callahan, Benjamin J., Caraballo-Rodríguez, Andrés Mauricio, Chase, John, Cope, Emily K., Da Silva, Ricardo, Diener, Christian, Dorrestein, Pieter C., Douglas, Gavin M., Durall, Daniel M., Duvallet, Claire, Edwardson, Christian F., Ernst, Madeleine, Estaki, Mehrbod, Fouquier, Jennifer, Gauglitz, Julia M., Gibbons, Sean M., Gibson, Deanna L., Gonzalez, Antonio, Gorlick, Kestrel, Guo, Jiarong, Hillmann, Benjamin, Holmes, Susan, Holste, Hannes, Huttenhower, Curtis, Huttley, Gavin A., Janssen, Stefan, Jarmusch, Alan K., Jiang, Lingjing, Kaehler, Benjamin D., Kang, Kyo Bin, Keefe, Christopher R., Keim, Paul, Kelley, Scott T., Knights, Dan, Koester, Irina, Kosciolek, Tomasz, Kreps, Jorden, Langille, Morgan G. I., Lee, Joslynn, Ley, Ruth, Liu, Yong-Xin, Loftfield, Erikka, Lozupone, Catherine, Maher, Massoud, Marotz, Clarisse, Martin, Bryan D., McDonald, Daniel, McIver, Lauren J., Melnik, Alexey V., Metcalf, Jessica L., Morgan, Sydney C., Morton, Jamie T., Naimey, Ahmad Turan, Navas-Molina, Jose A., Nothias, Louis Felix, Orchanian, Stephanie B., Pearson, Talima, Peoples, Samuel L., Petras, Daniel, Preuss, Mary Lai, Pruesse, Elmar, Rasmussen, Lasse Buur, Rivers, Adam, Robeson, II, Michael S., Rosenthal, Patrick, Segata, Nicola, Shaffer, Michael, Shiffer, Arron, Sinha, Rashmi, Song, Se Jin, Spear, John R., Swafford, Austin D., Thompson, Luke R., Torres, Pedro J., Trinh, Pauline, Tripathi, Anupriya, Turnbaugh, Peter J., Ul-Hasan, Sabah, van der Hooft, Justin J. J., Vargas, Fernando, Vázquez-Baeza, Yoshiki, Vogtmann, Emily, von Hippel, Max, Walters, William, Wan, Yunhu, Wang, Mingxun, Warren, Jonathan, Weber, Kyle C., Williamson, Charles H. D., Willis, Amy D., Xu, Zhenjiang Zech, Zaneveld, Jesse R., Zhang, Yilong, Zhu, Qiyun, Knight, Rob, and Caporaso, J. Gregory

Published
2019
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33. The gastrointestinal antibiotic resistome in pediatric leukemia and lymphoma patients.

Author

MacDonald, Tamara, Dunn, Katherine A., MacDonald, Jane, Langille, Morgan G. I., Van Limbergen, Johan E., Bielawski, Joseph P., and Kulkarni, Ketan

Subjects
CHILDHOOD cancer, ANTIBIOTICS, CANCER patients, FEBRILE neutropenia, SHOTGUN sequencing, GUT microbiome, RITUXIMAB
Abstract

Introduction: Most children with leukemia and lymphoma experience febrile neutropenia. These are treated with empiric antibiotics that include b-lactams and/or vancomycin. These are often administered for extended periods, and the effect on the resistome is unknown. Methods: We examined the impact of repeated courses and duration of antibiotic use on the resistome of 39 pediatric leukemia and lymphoma patients. Shotgun metagenome sequences from 127 stool samples of pediatric oncology patients were examined for abundance of antibiotic resistance genes (ARGs) in each sample. Abundances were grouped by repeated courses (no antibiotics, 1-2 courses, 3+ courses) and duration (no use, short duration, long and/or mixed durationg) of blactams, vancomycin and “any antibiotic” use. We assessed changes in both taxonomic composition and prevalence of ARGs among these groups. Results: We found that Bacteroidetes taxa and b-lactam resistance genes decreased, while opportunistic Firmicutes and Proteobacteria taxa, along with multidrug resistance genes, increased with repeated courses and/or duration of antibiotics. Efflux pump related genes predominated (92%) among the increased multidrug genes. While we found b-lactam ARGs present in the resistome, the taxa that appear to contain them were kept in check by antibiotic treatment. Multidrug ARGs, mostly efflux pumps or regulators of efflux pump genes, were associated with opportunistic pathogens, and both increased in the resistome with repeated antibiotic use and/or increased duration. Conclusions: Given the strong association between opportunistic pathogens and multidrug-related efflux pumps, we suggest that drug efflux capacity might allow the opportunistic pathogens to persist or increase despite repeated courses and/or duration of antibiotics. While drug efflux is the most direct explanation, other mechanisms that enhance the ability of opportunistic pathogens to handle environmental stress, or other aspects of the treatment environment, could also contribute to their ability to flourish within the gut during treatment. Persistence of opportunistic pathogens in an already dysbiotic and weakened gastrointestinal tract could increase the likelihood of lifethreatening blood borne infections. Of the 39 patients, 59% experienced at least one gastrointestinal or blood infection and 60% of bacteremia’s were bacteria found in stool samples. Antimicrobial stewardship and appropriate use and duration of antibiotics could help reduce morbidity and mortality in this vulnerable population. [ABSTRACT FROM AUTHOR]

Published
2023
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34. Gut bacterial gene changes following pegaspargase treatment in pediatric patients with acute lymphoblastic leukemia

Author

Dunn, Katherine A., primary, Forbrigger, Zara, additional, Connors, Jessica, additional, Rahman, Mushfiqur, additional, Cohen, Alejandro, additional, Van Limbergen, Johan, additional, Langille, Morgan G. I., additional, Stadnyk, Andrew W., additional, Bielawski, Joseph P., additional, Penny, Susanne L., additional, MacDonald, Tamara, additional, and Kulkarni, Ketan, additional

Published
2021
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36. A multi-OMIC characterisation of biodegradation and microbial community succession within the PET plastisphere

Author

Natural Environment Research Council (UK), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Commission, Ministerio de Economía y Competitividad (España), European Research Council, Wright, Robyn J., Bosch, Rafael, Langille, Morgan G. I., Gibson, Matthew I., Christie-Oleza, Joseph Alexander, Natural Environment Research Council (UK), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Commission, Ministerio de Economía y Competitividad (España), European Research Council, Wright, Robyn J., Bosch, Rafael, Langille, Morgan G. I., Gibson, Matthew I., and Christie-Oleza, Joseph Alexander

Abstract

[Background] Plastics now pollute marine environments across the globe. On entering these environments, plastics are rapidly colonised by a diverse community of microorganisms termed the plastisphere. Members of the plastisphere have a myriad of diverse functions typically found in any biofilm but, additionally, a number of marine plastisphere studies have claimed the presence of plastic-biodegrading organisms, although with little mechanistic verification. Here, we obtained a microbial community from marine plastic debris and analysed the community succession across 6 weeks of incubation with different polyethylene terephthalate (PET) products as the sole carbon source, and further characterised the mechanisms involved in PET degradation by two bacterial isolates from the plastisphere., [Results] We found that all communities differed significantly from the inoculum and were dominated by Gammaproteobacteria, i.e. Alteromonadaceae and Thalassospiraceae at early time points, Alcanivoraceae at later time points and Vibrionaceae throughout. The large number of encoded enzymes involved in PET degradation found in predicted metagenomes and the observation of polymer oxidation by FTIR analyses both suggested PET degradation was occurring. However, we were unable to detect intermediates of PET hydrolysis with metabolomic analyses, which may be attributed to their rapid depletion by the complex community. To further confirm the PET biodegrading potential within the plastisphere of marine plastic debris, we used a combined proteogenomic and metabolomic approach to characterise amorphous PET degradation by two novel marine isolates, Thioclava sp. BHET1 and Bacillus sp. BHET2. The identification of PET hydrolytic intermediates by metabolomics confirmed that both isolates were able to degrade PET. High-throughput proteomics revealed that whilst Thioclava sp. BHET1 used the degradation pathway identified in terrestrial environment counterparts, these were absent in Bacillus sp. BHET2, indicating that either the enzymes used by this bacterium share little homology with those characterised previously, or that this bacterium uses a novel pathway for PET degradation., [Conclusions] Overall, the results of our multi-OMIC characterisation of PET degradation provide a significant step forwards in our understanding of marine plastic degradation by bacterial isolates and communities and evidences the biodegrading potential extant in the plastisphere of marine plastic debris.

Published
2021

37. Correction to: A multi-OMIC characterisation of biodegradation and microbial community succession within the PET plastisphere

Author

Natural Environment Research Council (UK), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Commission, Ministerio de Economía y Competitividad (España), European Research Council, Wright, Robyn J., Bosch, Rafael, Langille, Morgan G. I., Gibson, Matthew I., Christie-Oleza, Joseph Alexander, Natural Environment Research Council (UK), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Commission, Ministerio de Economía y Competitividad (España), European Research Council, Wright, Robyn J., Bosch, Rafael, Langille, Morgan G. I., Gibson, Matthew I., and Christie-Oleza, Joseph Alexander

Abstract

[Background] Plastics now pollute marine environments across the globe. On entering these environments, plastics are rapidly colonised by a diverse community of microorganisms termed the plastisphere. Members of the plastisphere have a myriad of diverse functions typically found in any biofilm but, additionally, a number of marine plastisphere studies have claimed the presence of plastic-biodegrading organisms, although with little mechanistic verification. Here, we obtained a microbial community from marine plastic debris and analysed the community succession across 6 weeks of incubation with different polyethylene terephthalate (PET) products as the sole carbon source, and further characterised the mechanisms involved in PET degradation by two bacterial isolates from the plastisphere., [Results] We found that all communities differed significantly from the inoculum and were dominated by Gammaproteobacteria, i.e. Alteromonadaceae and Thalassospiraceae at early time points, Alcanivoraceae at later time points and Vibrionaceae throughout. The large number of encoded enzymes involved in PET degradation found in predicted metagenomes and the observation of polymer oxidation by FTIR analyses both suggested PET degradation was occurring. However, we were unable to detect intermediates of PET hydrolysis with metabolomic analyses, which may be attributed to their rapid depletion by the complex community. To further confirm the PET biodegrading potential within the plastisphere of marine plastic debris, we used a combined proteogenomic and metabolomic approach to characterise amorphous PET degradation by two novel marine isolates, Thioclava sp. BHET1 and Bacillus sp. BHET2. The identification of PET hydrolytic intermediates by metabolomics confirmed that both isolates were able to degrade PET. High-throughput proteomics revealed that whilst Thioclava sp. BHET1 used the degradation pathway identified in terrestrial environment counterparts, these were absent in Bacillus sp. BHET2, indicating that either the enzymes used by this bacterium share little homology with those characterised previously, or that this bacterium uses a novel pathway for PET degradation., [Conclusions] Overall, the results of our multi-OMIC characterisation of PET degradation provide a significant step forwards in our understanding of marine plastic degradation by bacterial isolates and communities and evidences the biodegrading potential extant in the plastisphere of marine plastic debris.

Published
2021

39. Antibiotic and antifungal use in pediatric leukemia and lymphoma patients are associated with increasing opportunistic pathogens and decreasing bacteria responsible for activities that enhance colonic defense.

Author

Dunn, Katherine A., MacDonald, Tamara, Rodrigues, Gloria J., Forbrigger, Zara, Bielawski, Joseph P., Langille, Morgan G. I., Limbergen, Johan Van, and Kulkarni, Ketan

Subjects
GUT microbiome, CHILDHOOD cancer, BUTYRATES, CHILD patients, CANCER patients, ANTIBIOTICS, ANTIFUNGAL agents
Abstract

Due to decreased immunity, both antibiotics and antifungals are regularly used in pediatric hematologic-cancer patients as a means to prevent severe infections and febrile neutropenia. The general effect of antibiotics on the human gut microbiome is profound, yielding decreased diversity and changes in community structure. However, the specific effect on pediatric oncology patients is not well-studied. The effect of antifungal use is even less understood, having been studied only in mouse models. Because the composition of the gut microbiome is associated with regulation of hematopoiesis, immune function and gastrointestinal integrity, changes within the patient gut can have implications for the clinical management of hematologic malignancies. The pediatric population is particularly challenging because the composition of the microbiome is age dependent, with some of the most pronounced changes occurring in the first three years of life. We investigated how antibiotic and antifungal use shapes the taxonomic composition of the stool microbiome in pediatric patients with leukemia and Frontiers in lymphoma, as inferred from both 16S rRNA and metagenome data. Associations with age, antibiotic use and antifungal use were investigated using multiple analysis methods. In addition, multivariable differential abundance was used to identify and assess specific taxa that were associated with multiple variables. Both antibiotics and antifungals were linked to a general decline in diversity in stool samples, which included a decrease in relative abundance in butyrate producers that play a critical role in host gut physiology (e.g., Faecalibacterium, Anaerostipes, Dorea, Blautia),. Furthermore, antifungal use was associated with a significant increase in relative abundance of opportunistic pathogens. Collectively, these findings have important implications for the treatment of leukemia and lymphoma patients. Butyrate is important for gastrointestinal integrity; it inhibits inflammation, reinforces colonic defense, mucosal immunity. and decreases oxidative stress. The routine use of broadspectrum anti-infectives in pediatric oncology patients could simultaneously contribute to a decline in gastrointestinal integrity and colonic defense while promoting increases in opportunistic pathogens within the patient gut. Because the gut microbiome has been linked to both short-term clinical outcomes, and longerlasting health effects, systematic characterization of the gut microbiome in pediatric patients during, and beyond, treatment is warranted. [ABSTRACT FROM AUTHOR]

Published
2022
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40. sj-pdf-1-ini-10.1177_1753425920980512 - Supplemental material for Transcriptomic profiling of Brassica napus responses to Pseudomonas aeruginosa

Author

Cook, Jamie, Douglas, Gavin M, Zhang, Janie, Glick, Bernard R, Langille, Morgan G I, Kun-Hsiang Liu, and Zhenyu Cheng

Subjects
FOS: Clinical medicine, fungi, food and beverages, 110306 Endocrinology
Abstract

Supplemental material, sj-pdf-1-ini-10.1177_1753425920980512 for Transcriptomic profiling of Brassica napus responses to Pseudomonas aeruginosa by Jamie Cook, Gavin M Douglas, Janie Zhang, Bernard R Glick, Morgan G, I Langille, Kun-Hsiang Liu and Zhenyu Cheng in Innate Immunity

Published
2020
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41. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Author

Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics, Bolyen, Evan, Rideout, Jai Ram, Dillon, Matthew R., Bokulich, Nicholas A., Abnet, Christian C., Al-Ghalith, Gabriel A., Alexander, Harriet, Alm, Eric J, Arumugam, Manimozhiyan, Asnicar, Francesco, Bai, Yang, Bisanz, Jordan E., Bittinger, Kyle, Brejnrod, Asker, Brislawn, Colin J., Brown, C. Titus, Callahan, Benjamin J., Caraballo-Rodríguez, Andrés Mauricio, Chase, John, Cope, Emily K., Da Silva, Ricardo, Diener, Christian, Dorrestein, Pieter C., Douglas, Gavin M., Durall, Daniel M., Duvallet, Claire, Edwardson, Christian F., Ernst, Madeleine, Estaki, Mehrbod, Fouquier, Jennifer, Gauglitz, Julia M., Gibbons, Sean M., Gibson, Deanna L., Gonzalez, Antonio, Gorlick, Kestrel, Guo, Jiarong, Hillmann, Benjamin, Holmes, Susan, Holste, Hannes, Huttenhower, Curtis, Huttley, Gavin A., Janssen, Stefan, Jarmusch, Alan K., Jiang, Lingjing, Kaehler, Benjamin D., Kang, Kyo Bin, Keefe, Christopher R., Keim, Paul, Kelley, Scott T., Knights, Dan, Koester, Irina, Kosciolek, Tomasz, Kreps, Jorden, Langille, Morgan G. I., Lee, Joslynn, Ley, Ruth, Liu, Yong-Xin, Loftfield, Erikka, Lozupone, Catherine, Maher, Massoud, Marotz, Clarisse, Martin, Bryan D., McDonald, Daniel, McIver, Lauren J., Melnik, Alexey V., Metcalf, Jessica L., Morgan, Sydney C., Morton, Jamie T., Naimey, Ahmad Turan, Navas-Molina, Jose A., Nothias, Louis Felix, Orchanian, Stephanie B., Pearson, Talima, Peoples, Samuel L., Petras, Daniel, Preuss, Mary Lai, Pruesse, Elmar, Rasmussen, Lasse Buur, Rivers, Adam, Robeson, Michael S., Rosenthal, Patrick, Segata, Nicola, Shaffer, Michael, Shiffer, Arron, Sinha, Rashmi, Song, Se Jin, Spear, John R., Swafford, Austin D., Thompson, Luke R., Torres, Pedro J., Trinh, Pauline, Tripathi, Anupriya, Turnbaugh, Peter J., Ul-Hasan, Sabah, van der Hooft, Justin J. J., Vargas, Fernando, Vázquez-Baeza, Yoshiki, Vogtmann, Emily, von Hippel, Max, Walters, William, Wan, Yunhu, Wang, Mingxun, Warren, Jonathan, Weber, Kyle C., Williamson, Charles H. D., Willis, Amy D., Xu, Zhenjiang Zech, Zaneveld, Jesse R., Zhang, Yilong, Zhu, Qiyun, Knight, Rob, Caporaso, J. Gregory, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics, Bolyen, Evan, Rideout, Jai Ram, Dillon, Matthew R., Bokulich, Nicholas A., Abnet, Christian C., Al-Ghalith, Gabriel A., Alexander, Harriet, Alm, Eric J, Arumugam, Manimozhiyan, Asnicar, Francesco, Bai, Yang, Bisanz, Jordan E., Bittinger, Kyle, Brejnrod, Asker, Brislawn, Colin J., Brown, C. Titus, Callahan, Benjamin J., Caraballo-Rodríguez, Andrés Mauricio, Chase, John, Cope, Emily K., Da Silva, Ricardo, Diener, Christian, Dorrestein, Pieter C., Douglas, Gavin M., Durall, Daniel M., Duvallet, Claire, Edwardson, Christian F., Ernst, Madeleine, Estaki, Mehrbod, Fouquier, Jennifer, Gauglitz, Julia M., Gibbons, Sean M., Gibson, Deanna L., Gonzalez, Antonio, Gorlick, Kestrel, Guo, Jiarong, Hillmann, Benjamin, Holmes, Susan, Holste, Hannes, Huttenhower, Curtis, Huttley, Gavin A., Janssen, Stefan, Jarmusch, Alan K., Jiang, Lingjing, Kaehler, Benjamin D., Kang, Kyo Bin, Keefe, Christopher R., Keim, Paul, Kelley, Scott T., Knights, Dan, Koester, Irina, Kosciolek, Tomasz, Kreps, Jorden, Langille, Morgan G. I., Lee, Joslynn, Ley, Ruth, Liu, Yong-Xin, Loftfield, Erikka, Lozupone, Catherine, Maher, Massoud, Marotz, Clarisse, Martin, Bryan D., McDonald, Daniel, McIver, Lauren J., Melnik, Alexey V., Metcalf, Jessica L., Morgan, Sydney C., Morton, Jamie T., Naimey, Ahmad Turan, Navas-Molina, Jose A., Nothias, Louis Felix, Orchanian, Stephanie B., Pearson, Talima, Peoples, Samuel L., Petras, Daniel, Preuss, Mary Lai, Pruesse, Elmar, Rasmussen, Lasse Buur, Rivers, Adam, Robeson, Michael S., Rosenthal, Patrick, Segata, Nicola, Shaffer, Michael, Shiffer, Arron, Sinha, Rashmi, Song, Se Jin, Spear, John R., Swafford, Austin D., Thompson, Luke R., Torres, Pedro J., Trinh, Pauline, Tripathi, Anupriya, Turnbaugh, Peter J., Ul-Hasan, Sabah, van der Hooft, Justin J. J., Vargas, Fernando, Vázquez-Baeza, Yoshiki, Vogtmann, Emily, von Hippel, Max, Walters, William, Wan, Yunhu, Wang, Mingxun, Warren, Jonathan, Weber, Kyle C., Williamson, Charles H. D., Willis, Amy D., Xu, Zhenjiang Zech, Zaneveld, Jesse R., Zhang, Yilong, Zhu, Qiyun, Knight, Rob, and Caporaso, J. Gregory

Published
2020

44. Investigating the gut microbial community and genes in children with differing levels of change in serum asparaginase activity during pegaspargase treatment for acute lymphoblastic leukemia

Author

Dunn, Katherine A., primary, Connors, Jessica, additional, Bielawski, Joseph P., additional, Nearing, Jacob T., additional, Langille, Morgan G. I., additional, Van Limbergen, Johan, additional, Fernandez, Conrad V., additional, MacDonald, Tamara, additional, and Kulkarni, Ketan, additional

Published
2020
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50. The human tumor microbiome is composed of tumor type–specific intracellular bacteria

Author

Nejman, Deborah, primary, Livyatan, Ilana, additional, Fuks, Garold, additional, Gavert, Nancy, additional, Zwang, Yaara, additional, Geller, Leore T., additional, Rotter-Maskowitz, Aviva, additional, Weiser, Roi, additional, Mallel, Giuseppe, additional, Gigi, Elinor, additional, Meltser, Arnon, additional, Douglas, Gavin M., additional, Kamer, Iris, additional, Gopalakrishnan, Vancheswaran, additional, Dadosh, Tali, additional, Levin-Zaidman, Smadar, additional, Avnet, Sofia, additional, Atlan, Tehila, additional, Cooper, Zachary A., additional, Arora, Reetakshi, additional, Cogdill, Alexandria P., additional, Khan, Md Abdul Wadud, additional, Ologun, Gabriel, additional, Bussi, Yuval, additional, Weinberger, Adina, additional, Lotan-Pompan, Maya, additional, Golani, Ofra, additional, Perry, Gili, additional, Rokah, Merav, additional, Bahar-Shany, Keren, additional, Rozeman, Elisa A., additional, Blank, Christian U., additional, Ronai, Anat, additional, Shaoul, Ron, additional, Amit, Amnon, additional, Dorfman, Tatiana, additional, Kremer, Ran, additional, Cohen, Zvi R., additional, Harnof, Sagi, additional, Siegal, Tali, additional, Yehuda-Shnaidman, Einav, additional, Gal-Yam, Einav Nili, additional, Shapira, Hagit, additional, Baldini, Nicola, additional, Langille, Morgan G. I., additional, Ben-Nun, Alon, additional, Kaufman, Bella, additional, Nissan, Aviram, additional, Golan, Talia, additional, Dadiani, Maya, additional, Levanon, Keren, additional, Bar, Jair, additional, Yust-Katz, Shlomit, additional, Barshack, Iris, additional, Peeper, Daniel S., additional, Raz, Dan J., additional, Segal, Eran, additional, Wargo, Jennifer A., additional, Sandbank, Judith, additional, Shental, Noam, additional, and Straussman, Ravid, additional

Published
2020
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