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  1. Article ; Online: Preservation of conjugated primary bile acids by oxygenation of the small intestinal microbiota

    Firrman, Jenni / Friedman, Elliot S / Hecht, Aaron / Strange, William C / Narrowe, Adrienne B / Mahalak, Karley / Wu, Gary D / Liu, LinShu

    mBio

    2024  , Page(s) e0094324

    Abstract: Bile acids play a critical role in the emulsification of dietary lipids, a critical step in the primary function of the small intestine, which is the digestion and absorption of food. Primary bile acids delivered into the small intestine are conjugated ... ...

    Abstract Bile acids play a critical role in the emulsification of dietary lipids, a critical step in the primary function of the small intestine, which is the digestion and absorption of food. Primary bile acids delivered into the small intestine are conjugated to enhance functionality, in part, by increasing aqueous solubility and preventing passive diffusion of bile acids out of the gut lumen. Bile acid function can be disrupted by the gut microbiota via the deconjugation of primary bile acids by bile salt hydrolases (BSHs), leading to their conversion into secondary bile acids through the expression of bacterial bile acid-inducible genes, a process often observed in malabsorption due to small intestinal bacterial overgrowth. By modeling the small intestinal microbiota
    Importance: Conjugated primary bile acids are produced by the liver and exist at high concentrations in the proximal small intestine, where they are critical for proper digestion. Deconjugation of these bile acids with subsequent transformation via dehydroxylation into secondary bile acids is regulated by the colonic gut microbiota and reduces their digestive function. Using an
    Language English
    Publishing date 2024-05-10
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2557172-2
    ISSN 2150-7511 ; 2161-2129
    ISSN (online) 2150-7511
    ISSN 2161-2129
    DOI 10.1128/mbio.00943-24
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Fructooligosaccharides (FOS) differentially modifies the

    Mahalak, Karley K / Firrman, Jenni / Narrowe, Adrienne B / Hu, Weiming / Jones, Steven M / Bittinger, Kyle / Moustafa, Ahmed M / Liu, LinShu

    Frontiers in nutrition

    2023  Volume 9, Page(s) 1058910

    Abstract: Introduction: Fructooligosaccharides (FOS) are well-known carbohydrates that promote healthy gut microbiota and have been previously demonstrated to enhance levels of : Methods: To address this concern, we implemented a 24-h : Results: These ... ...

    Abstract Introduction: Fructooligosaccharides (FOS) are well-known carbohydrates that promote healthy gut microbiota and have been previously demonstrated to enhance levels of
    Methods: To address this concern, we implemented a 24-h
    Results: These analyses found that FOS created a bifidogenic response in all age groups, increased overall SCFA levels, decreased alpha diversity, and shifted the communities to be more similar in beta diversity metrics. However, the age groups differed in which taxa were most prevalent or most affected by FOS treatment.
    Discussion: Overall, the results of this study demonstrate the positive effects of FOS on the gut microbiome, and importantly, how age may play a role in the effectiveness of this prebiotic.
    Language English
    Publishing date 2023-01-12
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2776676-7
    ISSN 2296-861X
    ISSN 2296-861X
    DOI 10.3389/fnut.2022.1058910
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Metagenomes and metagenome-assembled genomes from

    Narrowe, Adrienne B / Liu, LinShu / Lemons, Johanna M S / Firrman, Jenni A / Mahalak, Karley K / Deyaert, Stef / Baudot, Aurélien / Van den Abbeele, Pieter

    Microbiology resource announcements

    2024  Volume 13, Issue 2, Page(s) e0086223

    Abstract: We present a donor-specific collection of 78 metagenomes (13/donor) and 143 metagenome-assembled genomes (MAGs), representing the gut microbiomes of six healthy adult human donors. In addition to adding to the catalog of publicly available human gut MAGs, ...

    Abstract We present a donor-specific collection of 78 metagenomes (13/donor) and 143 metagenome-assembled genomes (MAGs), representing the gut microbiomes of six healthy adult human donors. In addition to adding to the catalog of publicly available human gut MAGs, this resource permits a genome-resolved look into microbial co-occurrence across six individuals.
    Language English
    Publishing date 2024-01-18
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/mra.00862-23
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Targeted remodeling of the human gut microbiome using Juemingzi (

    Narrowe, Adrienne B / Lemons, Johanna M S / Mahalak, Karley K / Firrman, Jenni / den Abbeele, Pieter Van / Baudot, Aurélien / Deyaert, Stef / Li, Yanfang / Yu, Liangli Lucy / Liu, LinShu

    Frontiers in cellular and infection microbiology

    2024  Volume 14, Page(s) 1296619

    Abstract: ... The ... ...

    Abstract The genus
    MeSH term(s) Humans ; Gastrointestinal Microbiome ; Senna Extract/analysis ; Senna Extract/pharmacology ; Microbiota ; Bacteria ; Feces/microbiology ; Seeds ; Sennosides/analysis ; Sennosides/pharmacology ; Anti-Infective Agents/pharmacology ; Drugs, Chinese Herbal
    Chemical Substances jueming ; Senna Extract (8013-11-4) ; Sennosides ; Anti-Infective Agents ; Drugs, Chinese Herbal
    Language English
    Publishing date 2024-04-04
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2619676-1
    ISSN 2235-2988 ; 2235-2988
    ISSN (online) 2235-2988
    ISSN 2235-2988
    DOI 10.3389/fcimb.2024.1296619
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Impact of Ivermectin on the Gut Microbial Ecosystem.

    Liu, LinShu / Mahalak, Karley K / Bobokalonov, Jamshed T / Narrowe, Adrienne B / Firrman, Jenni / Lemons, Johanna M S / Bittinger, Kyle / Hu, Weiming / Jones, Steven M / Moustafa, Ahmed M

    International journal of molecular sciences

    2023  Volume 24, Issue 22

    Abstract: Ivermectin is a an anti-helminthic that is critical globally for both human and veterinary care. To the best of our knowledge, information available regarding the influence of ivermectin (IVM) on the gut microbiota has only been collected from diseased ... ...

    Abstract Ivermectin is a an anti-helminthic that is critical globally for both human and veterinary care. To the best of our knowledge, information available regarding the influence of ivermectin (IVM) on the gut microbiota has only been collected from diseased donors, who were treated with IVM alone or in combination with other medicines. Results thus obtained were influenced by multiple elements beyond IVM, such as disease, and other medical treatments. The research presented here investigated the impact of IVM on the gut microbial structure established in a Triple-SHIME
    MeSH term(s) Adult ; Humans ; Feces ; Gastrointestinal Microbiome/genetics ; Ivermectin/pharmacology ; RNA, Ribosomal, 16S/genetics
    Chemical Substances Ivermectin (70288-86-7) ; RNA, Ribosomal, 16S
    Language English
    Publishing date 2023-11-09
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms242216125
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Methane-Oxidizing Activity Enhances Sulfamethoxazole Biotransformation in a Benthic Constructed Wetland Biomat.

    Vega, Michael A P / Scholes, Rachel C / Brady, Adam R / Daly, Rebecca A / Narrowe, Adrienne B / Vanzin, Gary F / Wrighton, Kelly C / Sedlak, David L / Sharp, Jonathan O

    Environmental science & technology

    2023  Volume 57, Issue 18, Page(s) 7240–7253

    Abstract: Ammonia monooxygenase and analogous oxygenase enzymes contribute to pharmaceutical biotransformation in activated sludge. In this study, we hypothesized that methane monooxygenase can enhance pharmaceutical biotransformation within the benthic, diffuse ... ...

    Abstract Ammonia monooxygenase and analogous oxygenase enzymes contribute to pharmaceutical biotransformation in activated sludge. In this study, we hypothesized that methane monooxygenase can enhance pharmaceutical biotransformation within the benthic, diffuse periphytic sediments (i.e., "biomat") of a shallow, open-water constructed wetland. To test this hypothesis, we combined field-scale metatranscriptomics, porewater geochemistry, and methane gas fluxes to inform microcosms targeting methane monooxygenase activity and its potential role in pharmaceutical biotransformation. In the field, sulfamethoxazole concentrations decreased within surficial biomat layers where genes encoding for the particulate methane monooxygenase (pMMO) were transcribed by a novel methanotroph classified as
    MeSH term(s) Wetlands ; Methane ; Oxidation-Reduction ; Minerals ; Biotransformation
    Chemical Substances Methane (OP0UW79H66) ; Minerals
    Language English
    Publishing date 2023-04-26
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, P.H.S. ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1520-5851
    ISSN (online) 1520-5851
    DOI 10.1021/acs.est.2c09314
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Impact of Baizhu, Daqingye, and Hehuanhua extracts on the human gut microbiome.

    Lemons, Johanna M S / Narrowe, Adrienne B / Liu, LinShu / Firrman, Jenni / Mahalak, Karley K / Van den Abbeele, Pieter / Baudot, Aurélien / Deyaert, Stef / Li, Yanfang / Yu, Liangli Lucy

    Frontiers in cellular and infection microbiology

    2023  Volume 13, Page(s) 1298392

    Abstract: Introduction: In traditional Chinese medicine, the rhizome of : Methods: As modulation of the human gut microbiome has been linked to host health status both within the gastrointestinal tract and in distant tissues, the effects of lipid-free ethanol ... ...

    Abstract Introduction: In traditional Chinese medicine, the rhizome of
    Methods: As modulation of the human gut microbiome has been linked to host health status both within the gastrointestinal tract and in distant tissues, the effects of lipid-free ethanol extracts of Baizhu, Daqingye, and Hehuanhua on the human adult gut microbiome were assessed using Systemic Intestinal Fermentation Research (SIFR
    Results and discussion: Baizhu and Daqingye extracts similarly impacted microbial community structure and function, with the extent of effects being more pronounced for Baizhu. These effects included decreases in the Bacteroidetes phylum and increases in health-related
    MeSH term(s) Humans ; Gastrointestinal Microbiome ; Drugs, Chinese Herbal/pharmacology ; Drugs, Chinese Herbal/chemistry ; Medicine, Chinese Traditional
    Chemical Substances Baizhu ; Drugs, Chinese Herbal
    Language English
    Publishing date 2023-12-07
    Publishing country Switzerland
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2619676-1
    ISSN 2235-2988 ; 2235-2988
    ISSN (online) 2235-2988
    ISSN 2235-2988
    DOI 10.3389/fcimb.2023.1298392
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Lacticaseibacillus rhamnosus

    Liu, LinShu / Narrowe, Adrienne B / Firrman, Jenni A / Mahalak, Karley K / Bobokalonov, Jamshed T / Lemons, Johanna M S / Bittinger, Kyle / Daniel, Scott / Tanes, Ceylan / Mattei, Lisa / Friedman, Elliot S / Soares, Jason W / Kobori, Masuko / Zeng, Wei-Bin / Tomasula, Peggy M

    Foods (Basel, Switzerland)

    2023  Volume 12, Issue 11

    Abstract: In the present research, we investigated changes in the gut metabolome that occurred in response to the administration of ... ...

    Abstract In the present research, we investigated changes in the gut metabolome that occurred in response to the administration of the
    Language English
    Publishing date 2023-05-24
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2704223-6
    ISSN 2304-8158
    ISSN 2304-8158
    DOI 10.3390/foods12112105
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Modulation of the Gut Microbiota Structure and Function by Two Structurally Different Lemon Pectins.

    Firrman, Jenni / Mahalak, Karley / Bobokalonov, Jamshed / Liu, LinShu / Lee, Jung-Jin / Bittinger, Kyle / Mattei, Lisa M / Gadaingan, Rizalina / Narrowe, Adrienne B / Lemons, Johanna M S

    Foods (Basel, Switzerland)

    2022  Volume 11, Issue 23

    Abstract: Pectins are plant polysaccharides consumed as part of a diet containing fruits and vegetables. Inside the gastrointestinal tract, pectin cannot be metabolized by the mammalian cells but is fermented by the gut microbiota in the colon with the subsequent ... ...

    Abstract Pectins are plant polysaccharides consumed as part of a diet containing fruits and vegetables. Inside the gastrointestinal tract, pectin cannot be metabolized by the mammalian cells but is fermented by the gut microbiota in the colon with the subsequent release of end products including short-chain fatty acids (SCFA). The prebiotic effects of pectin have been previously evaluated but reports are inconsistent, most likely due to differences in the pectin chemical structure which can vary by molecular weight (MW) and degree of esterification (DE). Here, the effects of two different MW lemon pectins with varying DEs on the gut microbiota of two donors were evaluated in vitro. The results demonstrated that low MW, high DE lemon pectin (LMW-HDE) altered community structure in a donor-dependent manner, whereas high MW, low DE lemon pectin (HMW-LDE) increased taxa within
    Language English
    Publishing date 2022-12-01
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2704223-6
    ISSN 2304-8158
    ISSN 2304-8158
    DOI 10.3390/foods11233877
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Pharmaceutical Biotransformation is Influenced by Photosynthesis and Microbial Nitrogen Cycling in a Benthic Wetland Biomat.

    Vega, Michael A P / Scholes, Rachel C / Brady, Adam R / Daly, Rebecca A / Narrowe, Adrienne B / Bosworth, Lily B / Wrighton, Kelly C / Sedlak, David L / Sharp, Jonathan O

    Environmental science & technology

    2022  Volume 56, Issue 20, Page(s) 14462–14477

    Abstract: In shallow, open-water engineered wetlands, design parameters select for a photosynthetic microbial biomat capable of robust pharmaceutical biotransformation, yet the contributions of specific microbial processes remain unclear. Here, we combined genome- ... ...

    Abstract In shallow, open-water engineered wetlands, design parameters select for a photosynthetic microbial biomat capable of robust pharmaceutical biotransformation, yet the contributions of specific microbial processes remain unclear. Here, we combined genome-resolved metatranscriptomics and oxygen profiling of a field-scale biomat to inform laboratory inhibition microcosms amended with a suite of pharmaceuticals. Our analyses revealed a dynamic surficial layer harboring oxic-anoxic cycling and simultaneous photosynthetic, nitrifying, and denitrifying microbial transcription spanning nine bacterial phyla, with unbinned eukaryotic scaffolds suggesting a dominance of diatoms. In the laboratory, photosynthesis, nitrification, and denitrification were broadly decoupled by incubating oxic and anoxic microcosms in the presence and absence of light and nitrogen cycling enzyme inhibitors. Through combining microcosm inhibition data with field-scale metagenomics, we inferred microbial clades responsible for biotransformation associated with membrane-bound nitrate reductase activity (emtricitabine, trimethoprim, and atenolol), nitrous oxide reduction (trimethoprim), ammonium oxidation (trimethoprim and emtricitabine), and photosynthesis (metoprolol). Monitoring of transformation products of atenolol and emtricitabine confirmed that inhibition was specific to biotransformation and highlighted the value of oscillating redox environments for the further transformation of atenolol acid. Our findings shed light on microbial processes contributing to pharmaceutical biotransformation in open-water wetlands with implications for similar nature-based treatment systems.
    MeSH term(s) Ammonium Compounds ; Atenolol ; Biotransformation ; Denitrification ; Emtricitabine/metabolism ; Metoprolol ; Nitrate Reductases/metabolism ; Nitrification ; Nitrogen/metabolism ; Nitrous Oxide ; Oxygen ; Pharmaceutical Preparations ; Photosynthesis ; Trimethoprim ; Water ; Wetlands
    Chemical Substances Ammonium Compounds ; Pharmaceutical Preparations ; Water (059QF0KO0R) ; Atenolol (50VV3VW0TI) ; Trimethoprim (AN164J8Y0X) ; Nitrate Reductases (EC 1.7.-) ; Emtricitabine (G70B4ETF4S) ; Metoprolol (GEB06NHM23) ; Nitrous Oxide (K50XQU1029) ; Nitrogen (N762921K75) ; Oxygen (S88TT14065)
    Language English
    Publishing date 2022-10-05
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1520-5851
    ISSN (online) 1520-5851
    DOI 10.1021/acs.est.2c03566
    Database MEDical Literature Analysis and Retrieval System OnLINE

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