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Book ; Online ; Conference proceedings: Nutrition, Gut Microbiota and Immunity: Therapeutic Targets for IBD

Lewis, J.D.

79th Nestlé Nutrition Institute Workshop, New York, N.Y., September 2013

(Nestlé Nutrition Institute Workshop Series ; Vol.79)

2014

Series title	Nestlé Nutrition Institute Workshop Series ; Vol.79
Keywords	Gastroenterology ; Nutrition ; Immunology
Language	English
Size	1 Online-Ressource (XIV + 166 S.)
Publisher	S. Karger
Publishing place	Basel
Document type	Book ; Online ; Conference proceedings
Note	A comprehensive review
HBZ-ID	HT019543343
ISBN	978-3-318-02670-2 ; 3-318-02670-0
Database	ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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Article ; Online: Contraction-associated maternal heart rate decelerations ameliorated by phenylephrine infusion in a hypovolemic but fluid-restricted patient with pneumonia and pericardial effusion.

Lewis, J D / Archer, T L

International journal of obstetric anesthesia

2021 Volume 50, Page(s) 103250

MeSH term(s)	Deceleration ; Heart Rate ; Humans ; Hypovolemia ; Pericardial Effusion/therapy ; Phenylephrine/therapeutic use ; Pneumonia
Chemical Substances	Phenylephrine (1WS297W6MV)
Language	English
Publishing date	2021-12-30
Publishing country	Netherlands
Document type	Letter
ZDB-ID	1086024-1
ISSN	1532-3374 ; 0959-289X
ISSN (online)	1532-3374
ISSN	0959-289X
DOI	10.1016/j.ijoa.2021.103250
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.A 3311: Show issues

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Article ; Online: Preferential associations of soil fungal taxa under mixed compositions of eastern American tree species.

Kutos, Steve / Barnes, Elle M / Bhutada, Arnav / Lewis, J D

FEMS microbiology ecology

2022 Volume 98, Issue 6

Abstract: Soil fungi are vital to forest ecosystem function, in part through their role mediating tree responses to environmental factors, as well as directly through effects on resource cycling. While the distribution of soil fungi can vary with abiotic factors, ... ...

Abstract	Soil fungi are vital to forest ecosystem function, in part through their role mediating tree responses to environmental factors, as well as directly through effects on resource cycling. While the distribution of soil fungi can vary with abiotic factors, plant species identity is also known to affect community composition. However, the particular influence that a plant will have on its soil microbiota remains difficult to predict. Here, we paired amplicon sequencing and enzymatic assays to assess soil fungal composition and function under three tree species, Quercus rubra, Betula nigra, and Acer rubrum, planted individually and in all combinations in a greenhouse. We observed that fungal communities differed between each of the individual planted trees, suggesting at least some fungal taxa may associate preferentially with these tree species. Additionally, fungal community composition under mixed-tree plantings broadly differed from the individual planted trees, suggesting mixing of these distinct soil fungal communities. The data also suggest that there were larger enzymatic activities in the individual plantings as compared to all mixed-tree plantings which may be due to variations in fungal community composition. This study provides further evidence of the importance of tree identity on soil microbiota and functional changes to forest soils.
MeSH term(s)	Ecosystem ; Forests ; Fungi/classification ; Fungi/genetics ; Fungi/metabolism ; Microbiota/physiology ; Plants/metabolism ; Plants/microbiology ; Soil/chemistry ; Soil Microbiology ; Symbiosis/physiology ; Trees/microbiology
Chemical Substances	Soil
Language	English
Publishing date	2022-05-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	283722-5
ISSN	1574-6941 ; 0168-6496
ISSN (online)	1574-6941
ISSN	0168-6496
DOI	10.1093/femsec/fiac056
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Zs.A 2967: Show issues

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Article ; Online: Letter: the safety of herpes zoster vaccination for patients with inflammatory bowel disease being treated with anti-TNF medications-authors' reply.

Khan, N / Lewis, J D

Alimentary pharmacology & therapeutics

2018 Volume 47, Issue 3, Page(s) 448

MeSH term(s)	Herpes Zoster ; Humans ; Inflammatory Bowel Diseases ; Tumor Necrosis Factor-alpha ; Vaccination
Chemical Substances	Tumor Necrosis Factor-alpha
Language	English
Publishing date	2018-01-31
Publishing country	England
Document type	Letter ; Comment
ZDB-ID	639012-2
ISSN	1365-2036 ; 0269-2813 ; 0953-0673
ISSN (online)	1365-2036
ISSN	0269-2813 ; 0953-0673
DOI	10.1111/apt.14460
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Zs.A 2206: Show issues

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Article: Predicting Microbiome Function Across Space Is Confounded by Strain-Level Differences and Functional Redundancy Across Taxa.

Barnes, Elle M / Carter, Erin L / Lewis, J D

Frontiers in microbiology

2020 Volume 11, Page(s) 101

Abstract: Variation in the microbiome among individual organisms may play a critical role in the relative susceptibility of those organisms to infection, disease, and death. However, predicting microbiome function is difficult because of spatial and temporal ... ...

Abstract	Variation in the microbiome among individual organisms may play a critical role in the relative susceptibility of those organisms to infection, disease, and death. However, predicting microbiome function is difficult because of spatial and temporal variation in microbial diversity, and taxonomic diversity is not predictive of microbiome functional diversity. Addressing this issue may be particularly important when addressing pandemic diseases, such as the global amphibian die-off associated with
Language	English
Publishing date	2020-02-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2020.00101
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Article: Assembly of the amphibian microbiome is influenced by the effects of land‐use change on environmental reservoirs

Barnes, Elle M. / Kutos, Steve / Naghshineh, Nina / Mesko, Marissa / You, Qing / Lewis, J. D.

Environmental microbiology. 2021 Aug., v. 23, no. 8

2021

Abstract: A growing focus in microbial ecology is understanding how beneficial microbiome function is created and maintained through various assembly mechanisms. This study explores the role of both the environment and disease in regulating the composition of ... ...

Abstract	A growing focus in microbial ecology is understanding how beneficial microbiome function is created and maintained through various assembly mechanisms. This study explores the role of both the environment and disease in regulating the composition of microbial species in the soil and on amphibian hosts. We compared the microbial communities of Plethodon cinereus salamanders along a land‐use gradient in the New York metropolitan area and paired these with associated soil cores. Additionally, we characterized the diversity of bacterial and fungal symbionts that putatively inhibit the pathogenic fungus Batrachochytrium dendrobatidis. We predicted that variation in skin microbial community composition would correlate with changes seen in the soil which functions as the regional species pool. We found that salamanders and soil share many microbial taxa but that these two communities exhibit differences in the relative abundances of the bacterial phyla Acidobacteria, Actinobacteria, and Proteobacteria and the fungal phyla Ascomycota and genus Basidiobolus. Microbial community composition varies with changes in land‐use associated factors creating site‐specific compositions. By employing a quantitative, null‐based assembly model, we identified that dispersal limitation, variable selection, and drift guide assembly of microbes onto their skin, creating high dissimilarity between individuals with likely consequences in disease preventative function.
Keywords	Acidobacteria ; Actinobacteria ; Ascomycota ; Basidiobolus ; Batrachochytrium dendrobatidis ; Plethodon cinereus ; Proteobacteria ; community structure ; fungi ; land use change ; metropolitan areas ; microbial communities ; microbiome ; models ; soil ; symbionts ; virulent strains ; New York
Language	English
Dates of publication	2021-08
Size	p. 4595-4611.
Publishing place	John Wiley & Sons, Inc.
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.15653
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Assembly of the amphibian microbiome is influenced by the effects of land-use change on environmental reservoirs.

Barnes, Elle M / Kutos, Steve / Naghshineh, Nina / Mesko, Marissa / You, Qing / Lewis, J D

Environmental microbiology

2021 Volume 23, Issue 8, Page(s) 4595–4611

Abstract	A growing focus in microbial ecology is understanding how beneficial microbiome function is created and maintained through various assembly mechanisms. This study explores the role of both the environment and disease in regulating the composition of microbial species in the soil and on amphibian hosts. We compared the microbial communities of Plethodon cinereus salamanders along a land-use gradient in the New York metropolitan area and paired these with associated soil cores. Additionally, we characterized the diversity of bacterial and fungal symbionts that putatively inhibit the pathogenic fungus Batrachochytrium dendrobatidis. We predicted that variation in skin microbial community composition would correlate with changes seen in the soil which functions as the regional species pool. We found that salamanders and soil share many microbial taxa but that these two communities exhibit differences in the relative abundances of the bacterial phyla Acidobacteria, Actinobacteria, and Proteobacteria and the fungal phyla Ascomycota and genus Basidiobolus. Microbial community composition varies with changes in land-use associated factors creating site-specific compositions. By employing a quantitative, null-based assembly model, we identified that dispersal limitation, variable selection, and drift guide assembly of microbes onto their skin, creating high dissimilarity between individuals with likely consequences in disease preventative function.
MeSH term(s)	Amphibians ; Animals ; Bacteria/genetics ; Fungi/genetics ; Humans ; Microbiota ; Soil Microbiology
Language	English
Publishing date	2021-07-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.15653
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Comparison of risk factors and outcomes of daptomycin-susceptible and -nonsusceptible vancomycin-resistant Enterococcus faecium infections in liver transplant recipients.

Lewis, J D / Barros, A J / Sifri, C D

Transplant infectious disease : an official journal of the Transplantation Society

2018 Volume 20, Issue 3, Page(s) e12856

Abstract: Background: Vancomycin-resistant Enterococcus faecium (VRE) infections are common in liver transplant recipients (LTRs). Daptomycin (DAP) is an important treatment for such infections; however, DAP-nonsusceptible VRE (DNS-VRE) are increasingly frequent. ...

Abstract	Background: Vancomycin-resistant Enterococcus faecium (VRE) infections are common in liver transplant recipients (LTRs). Daptomycin (DAP) is an important treatment for such infections; however, DAP-nonsusceptible VRE (DNS-VRE) are increasingly frequent. The purpose of this study was to compare clinical characteristics and outcomes of LTRs with infections due to DNS-VRE and DAP-susceptible VRE (DS-VRE). Methods: A single center, retrospective review of patients who underwent liver transplantation between January 1, 2010 and December 31, 2015 and developed infections due to DS-VRE or DNS-VRE post transplant was performed. Patients with DNS-VRE and DS-VRE infections were compared using univariate and logistic regression analysis. Results: Fourteen LTRs developed DNS-VRE and 20 LTRs developed DS-VRE infection post-transplantation. No significant differences were observed in demographics, model for end-stage liver disease (MELD) scores, causes of end-stage liver disease, or rate of pre-transplant perirectal VRE colonization between groups. Bleeding complications and renal replacement therapy were more common in the DNS-VRE group than in the DS-VRE group. The duration of transplant hospitalization and post-transplant intensive care unit (ICU) admission was longer in the DNS-VRE group than in the DS-VRE group. The 30-day and 6-month mortality rate associated with DNS-VRE infection was similar to that associated with DS-VRE infection. Conclusions: Liver transplant recipients who develop DNS-VRE infection have higher bleeding complications and longer, more complex hospitalizations compared to those who develop DS-VRE infection post transplantation; however, mortality at 30 days and 6 months is not significantly worse. Further study is needed to determine optimal strategies for the prevention and treatment of DNS-VRE infections in LTRs.
MeSH term(s)	Adult ; Aged ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Daptomycin/pharmacology ; Daptomycin/therapeutic use ; Enterococcus faecium/drug effects ; Female ; Gram-Positive Bacterial Infections/drug therapy ; Gram-Positive Bacterial Infections/epidemiology ; Gram-Positive Bacterial Infections/etiology ; Humans ; Liver/drug effects ; Liver Transplantation/adverse effects ; Male ; Middle Aged ; Retrospective Studies ; Risk Factors ; Vancomycin/pharmacology ; Vancomycin/therapeutic use ; Vancomycin-Resistant Enterococci/drug effects ; Vancomycin-Resistant Enterococci/isolation & purification ; Vancomycin-Resistant Enterococci/physiology
Chemical Substances	Anti-Bacterial Agents ; Vancomycin (6Q205EH1VU) ; Daptomycin (NWQ5N31VKK)
Language	English
Publishing date	2018-04-16
Publishing country	Denmark
Document type	Comparative Study ; Journal Article
ZDB-ID	1476094-0
ISSN	1399-3062 ; 1398-2273
ISSN (online)	1399-3062
ISSN	1398-2273
DOI	10.1111/tid.12856
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.A 5100: Show issues

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Article: Introduced and native plant species composition of vacant unmanaged green roofs in New York City

Aloisio, Jason M / Palmer, Matthew I / Tuininga, Amy R / Lewis, J. D

Urban ecosystems. 2020 Dec., v. 23, no. 6

2020

Abstract: Vacant spaces, such as unplanted, unmanaged, or infrequently accessed green roofs, may play a critical role in sustaining biodiversity in cities. Initial plant composition of these spaces likely is contingent on seed dispersal and growing medium, yet no ... ...

Abstract	Vacant spaces, such as unplanted, unmanaged, or infrequently accessed green roofs, may play a critical role in sustaining biodiversity in cities. Initial plant composition of these spaces likely is contingent on seed dispersal and growing medium, yet no studies have directly characterized the effects of location or growing medium depth on plant diversity of unplanted green roofs. To address this gap, we studied first-year community composition of five unplanted green roofs in New York City (NY, USA). On each roof, 12 plots were established with media depths ranging from 5 to 13 cm. Four months after installation, all plants were harvested. We observed 29 species across locations; five species were found on all five roofs, while 13 species each were observed on a single roof. Introduced species accounted for 14 of the 29 species found across roofs. Species richness and composition differed among roofs, while functional richness varied within, but not among, roofs. About 80% of the variation in species richness was accounted for by total green space in the neighborhoods within 100 to 200 m of each roof. Functional richness and plant cover increased with increased growing medium depth, as did the relative abundance of annual and forb species. Our results suggest both location and growing medium depth will affect initial community composition of unmanaged green roofs, but with differential effects on community assembly. These results also highlight the potential role of unmanaged vacant roofs as reservoirs of plant diversity, both native and invasive, in urban spaces.
Keywords	community structure ; forbs ; indigenous species ; introduced species ; seed dispersal ; species richness ; New York
Language	English
Dates of publication	2020-12
Size	p. 1227-1238.
Publishing place	Springer US
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2019257-5
ISSN	1573-1642 ; 1083-8155
ISSN (online)	1573-1642
ISSN	1083-8155
DOI	10.1007/s11252-020-00992-6
Database	NAL-Catalogue (AGRICOLA)

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Article: A Rapid Seedling Resistance Assay Identifies Wild Tomato Lines That Are Resistant to Pseudomonas syringae pv. tomato Race 1.

Hassan, J A / Zhou, Y J / Lewis, J D

Molecular plant-microbe interactions : MPMI

2017 Volume 30, Issue 9, Page(s) 701–709

Abstract: Bacterial speck caused by Pseudomonas syringae has historically been controlled by the Pto/Prf gene cluster. Emerging strains like P. syringae pv. tomato race 1 overcome resistance conferred by Pto/Prf, and can cause serious crop loss under appropriate ... ...

Abstract	Bacterial speck caused by Pseudomonas syringae has historically been controlled by the Pto/Prf gene cluster. Emerging strains like P. syringae pv. tomato race 1 overcome resistance conferred by Pto/Prf, and can cause serious crop loss under appropriate environmental conditions. We developed a rapid assay to screen wild tomato seedlings for resistance to P. syringae pv. tomato race 1. We established the seedling resistance assay using the well-characterized P. syringae pv. tomato race 0 strain, DC3000, which is recognized in tomato cultivars carrying Pto/Prf (PtoR) and causes disease in isogenic lines lacking this cluster (PtoS). We optimized infectious conditions for P. syringae on tomato seedlings and demonstrated that tomato seedlings respond like adult tomato plants in critical measures of susceptibility and immunity, including the hypersensitive response, rapid ion leakage, restricted bacterial proliferation, and phenotypic resistance. After establishing infectious conditions for P. syringae pv. tomato race 1 on tomato seedlings, we screened 96 wild accessions and identified two accessions with strong P. syringae pv. tomato race 1 resistance, Solanum neorickii LA1329 and S. habrochaites LA1253, which are also resistant to bacterial infection as adult plants. This rapid high throughput seedling assay has many advantages, including reduced plant growth time and large sample sizes, and will allow for large-scale screening of resistance in tomato.
Language	English
Publishing date	2017-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	743331-1
ISSN	1943-7706 ; 0894-0282
ISSN (online)	1943-7706
ISSN	0894-0282
DOI	10.1094/MPMI-11-16-0247-R
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Zs.A 3530: Show issues

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