Search

Your search keyword '"Rimal, Bipin"' showing total 32 results
Start Over Author "Rimal, Bipin"
32 results on '"Rimal, Bipin"'

1. Effects of Early Life Exposures to the Aryl Hydrocarbon Receptor Ligand TCDF on Gut Microbiota and Host Metabolic Homeostasis in C57BL/6J Mice

Author

Tian, Yuan, Rimal, Bipin, Bisanz, Jordan E., Gui, Wei, Wolfe, Trenton M., Koo, Imhoi, Murray, Iain A., Nettleford, Shaneice K., Yokoyama, Shigetoshi, Dong, Fangcong, Koshkin, Sergei, Prabhu, K. Sandeep, Turnbaugh, Peter J., Walk, Seth T., Perdew, Gary H., and Patterson, Andrew D.

Subjects
Metabolism -- Environmental aspects -- Health aspects, Microbiota (Symbiotic organisms) -- Physiological aspects -- Environmental aspects -- Health aspects, Hydrocarbons -- Physiological aspects -- Health aspects, Homeostasis -- Environmental aspects, Persistent organic pollutants -- Physiological aspects -- Health aspects
Abstract

BACKGROUND: Exposure to persistent organic pollutants (POPs) and disruptions in the gastrointestinal microbiota have been positively correlated with a predisposition to factors such as obesity, metabolic syndrome, and type 2 diabetes; however, it is unclear how the microbiome contributes to this relationship. OBJECTIVE: This study aimed to explore the association between early life exposure to a potent aryl hydrocarbon receptor (AHR) agonist and persistent disruptions in the microbiota, leading to impaired metabolic homeostasis later in life. METHODS: This study used metagenomics, nuclear magnetic resonance (NMR)- and mass spectrometry (MS)-based metabolomics, and biochemical assays to analyze the gut microbiome composition and function, as well as the physiological and metabolic effects of early life exposure to 2,3,7,8-tetrachlorodibenzofuran (TCDF) in conventional, germ-free (GF), and Ahr-null mice. The impact of TCDF on Akkermansia muciniphila (A. muciniphila) in vitro was assessed using optical density (OD 600), flow cytometry, transcriptomics, and MS-based metabolomics. RESULTS: TCDF-exposed mice exhibited lower abundances of A. muciniphila, lower levels of cecal short-chain fatty acids (SCFAs) and indole-3-lactic acid (ILA), as well as lower levels of the gut hormones glucagon-like peptide 1 (GLP-1) and peptide YY (PYY), findings suggestive of disruption in the gut microbiome community structure and function. Importantly, microbial and metabolic phenotypes associated with early life POP exposure were transferable to GF recipients in the absence of POP carry-over. In addition, AHR-independent interactions between POPs and the microbiota were observed, and they were significantly associated with growth, physiology, gene expression, and metabolic activity outcomes of A. muciniphila, supporting suppressed activity along the ILA pathway. CONCLUSIONS: These data obtained in a mouse model point to the complex effects of POPs on the host and microbiota, providing strong evidence that early life, short-term, and self-limiting POP exposure can adversely impact the microbiome, with effects persisting into later life with associated health implications. https://doi.org/10.1289/EHP13356, Introduction Persistent organic pollutants (POPs) are a serious and global threat to human health owing to their persistence, prevalence, and bioaccumulative nature. Exposure to POPs is associated with various health [...]

Published
2024
Full Text
View/download PDF

2. microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data

Author

Zuffa, Simone, Schmid, Robin, Bauermeister, Anelize, P. Gomes, Paulo Wender, Caraballo-Rodriguez, Andres M, El Abiead, Yasin, Aron, Allegra T, Gentry, Emily C, Zemlin, Jasmine, Meehan, Michael J, Avalon, Nicole E, Cichewicz, Robert H, Buzun, Ekaterina, Terrazas, Marvic Carrillo, Hsu, Chia-Yun, Oles, Renee, Ayala, Adriana Vasquez, Zhao, Jiaqi, Chu, Hiutung, Kuijpers, Mirte CM, Jackrel, Sara L, Tugizimana, Fidele, Nephali, Lerato Pertunia, Dubery, Ian A, Madala, Ntakadzeni Edwin, Moreira, Eduarda Antunes, Costa-Lotufo, Leticia Veras, Lopes, Norberto Peporine, Rezende-Teixeira, Paula, Jimenez, Paula C, Rimal, Bipin, Patterson, Andrew D, Traxler, Matthew F, Pessotti, Rita de Cassia, Alvarado-Villalobos, Daniel, Tamayo-Castillo, Giselle, Chaverri, Priscila, Escudero-Leyva, Efrain, Quiros-Guerrero, Luis-Manuel, Bory, Alexandre Jean, Joubert, Juliette, Rutz, Adriano, Wolfender, Jean-Luc, Allard, Pierre-Marie, Sichert, Andreas, Pontrelli, Sammy, Pullman, Benjamin S, Bandeira, Nuno, Gerwick, William H, Gindro, Katia, Massana-Codina, Josep, Wagner, Berenike C, Forchhammer, Karl, Petras, Daniel, Aiosa, Nicole, Garg, Neha, Liebeke, Manuel, Bourceau, Patric, Kang, Kyo Bin, Gadhavi, Henna, de Carvalho, Luiz Pedro Sorio, Silva dos Santos, Mariana, Pérez-Lorente, Alicia Isabel, Molina-Santiago, Carlos, Romero, Diego, Franke, Raimo, Brönstrup, Mark, Vera Ponce de León, Arturo, Pope, Phillip Byron, La Rosa, Sabina Leanti, La Barbera, Giorgia, Roager, Henrik M, Laursen, Martin Frederik, Hammerle, Fabian, Siewert, Bianka, Peintner, Ursula, Licona-Cassani, Cuauhtemoc, Rodriguez-Orduña, Lorena, Rampler, Evelyn, Hildebrand, Felina, Koellensperger, Gunda, Schoeny, Harald, Hohenwallner, Katharina, Panzenboeck, Lisa, Gregor, Rachel, O’Neill, Ellis Charles, Roxborough, Eve Tallulah, Odoi, Jane, Bale, Nicole J, Ding, Su, Sinninghe Damsté, Jaap S, Guan, Xue Li, Cui, Jerry J, Ju, Kou-San, Silva, Denise Brentan, Silva, Fernanda Motta Ribeiro, da Silva, Gilvan Ferreira, Koolen, Hector HF, Grundmann, Carlismari, and Clement, Jason A

Subjects
Microbiology, Biological Sciences, Good Health and Well Being, Humans, Tandem Mass Spectrometry, Metabolomics, Databases, Factual, Medical Microbiology
Abstract

microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbe-derived metabolites and relative producers without a priori knowledge will vastly enhance the understanding of microorganisms' role in ecology and human health.

Published
2024

3. Bile salt hydrolase catalyses formation of amine-conjugated bile acids

Author

Rimal, Bipin, Collins, Stephanie L., Tanes, Ceylan E., Rocha, Edson R., Granda, Megan A., Solanki, Sumeet, Hoque, Nushrat J., Gentry, Emily C., Koo, Imhoi, Reilly, Erin R., Hao, Fuhua, Paudel, Devendra, Singh, Vishal, Yan, Tingting, Kim, Min Soo, Bittinger, Kyle, Zackular, Joseph P., Krausz, Kristopher W., Desai, Dhimant, Amin, Shantu, Coleman, James P., Shah, Yatrik M., Bisanz, Jordan E., Gonzalez, Frank J., Vanden Heuvel, John P., Wu, Gary D., Zemel, Babette S., Dorrestein, Pieter C., Weinert, Emily E., and Patterson, Andrew D.

Published
2024
Full Text
View/download PDF

6. Methotrexate impacts conserved pathways in diverse human gut bacteria leading to decreased host immune activation

Author

Nayak, Renuka R, Alexander, Margaret, Deshpande, Ishani, Stapleton-Gray, Kye, Rimal, Bipin, Patterson, Andrew D, Ubeda, Carles, Scher, Jose U, and Turnbaugh, Peter J

Subjects
Microbiology, Biological Sciences, Biomedical and Clinical Sciences, Arthritis, Autoimmune Disease, Women's Health, Microbiome, Rheumatoid Arthritis, Clinical Research, Infection, Oral and gastrointestinal, Inflammatory and immune system, Good Health and Well Being, Animals, Arthritis, Rheumatoid, Autoimmune Diseases, Bacteria, Female, Gastrointestinal Microbiome, Gastrointestinal Tract, Humans, Metabolomics, Methotrexate, Mice, Mice, Inbred C57BL, Phylogeny, Purines, Pyrimidines, RNA, Ribosomal, 16S, Tetrahydrofolate Dehydrogenase, Transcriptome, DMARD, autoimmune disease, human gut microbiome, immune activation, metabolomics, methotrexate, microbiota, off-target effects, purine and pyrimidine biosynthesis, rheumatoid arthritis, Medical Microbiology, Immunology, Biochemistry and cell biology, Medical microbiology
Abstract

Immunomodulatory drugs can inhibit bacterial growth, yet their mechanism of action, spectrum, and clinical relevance remain unknown. Methotrexate (MTX), a first-line rheumatoid arthritis (RA) treatment, inhibits mammalian dihydrofolate reductase (DHFR), but whether it directly impacts gut bacteria is unclear. We show that MTX broadly alters the human gut microbiota. Drug sensitivity varied across strains, but the mechanism of action against DHFR appears conserved between mammalian and bacterial cells. RA patient microbiotas were sensitive to MTX, and changes in gut bacterial taxa and gene family abundance were distinct between responders and non-responders. Transplantation of post-treatment samples into germ-free mice given an inflammatory trigger led to reduced immune activation relative to pre-treatment controls, enabling identification of MTX-modulated bacterial taxa associated with intestinal and splenic immune cells. Thus, conservation in cellular pathways across domains of life can result in broad off-target drug effects on the human gut microbiota with consequences for immune function.

Published
2021

7. microbeMASST:a taxonomically informed mass spectrometry search tool for microbial metabolomics data

Author

Zuffa, Simone, Schmid, Robin, Bauermeister, Anelize, Paulo, Paulo Wender, Caraballo-Rodriguez, Andres M., El Abiead, Yasin, Aron, Allegra T., Gentry, Emily C., Zemlin, Jasmine, Meehan, Michael J., Avalon, Nicole E., Cichewicz, Robert H., Buzun, Ekaterina, Terrazas, Marvic Carrillo, Hsu, Chia Yun, Oles, Renee, Ayala, Adriana Vasquez, Zhao, Jiaqi, Chu, Hiutung, Kuijpers, Mirte C.M., Jackrel, Sara L., Tugizimana, Fidele, Nephali, Lerato Pertunia, Dubery, Ian A., Madala, Ntakadzeni Edwin, Moreira, Eduarda Antunes, Costa-Lotufo, Leticia Veras, Lopes, Norberto Peporine, Rezende-Teixeira, Paula, Jimenez, Paula C., Rimal, Bipin, Patterson, Andrew D., Traxler, Matthew F., Pessotti, Rita de Cassia, Alvarado-Villalobos, Daniel, Tamayo-Castillo, Giselle, Chaverri, Priscila, Escudero-Leyva, Efrain, Quiros-Guerrero, Luis Manuel, Bory, Alexandre Jean, Joubert, Juliette, Rutz, Adriano, Wolfender, Jean-Luc, Allard, Pierre-Marie, Sichert, Andreas, Pontrelli, Sammy, Pullman, Benjamin S., Bandeira, Nuno, Gerwick, William H., Gindro, Katia, Massana-Codina, Josep, Wagner, Berenike C., Forchhammer, Karl, Petras, Daniel, Aiosa, Nicole, Garg, Neha, Liebeke, Manuel, Bourceau, Patric, Kang, Kyo Bin, Gadhavi, Henna, de Carvalho, Luiz Pedro Sorio, Silva dos Santos, Mariana, Pérez-Lorente, Alicia Isabel, Molina-Santiago, Carlos, Romero, Diego, Franke, Raimo, Brönstrup, Mark, Vera Ponce de León, Arturo, Pope, Phillip Byron, La Rosa, Sabina Leanti, La Barbera, Giorgia, Roager, Henrik M., Laursen, Martin Frederik, Hammerle, Fabian, Siewert, Bianka, Peintner, Ursula, Licona-Cassani, Cuauhtemoc, Rodriguez-Orduña, Lorena, Rampler, Evelyn, Hildebrand, Felina, Koellensperger, Gunda, Schoeny, Harald, Hohenwallner, Katharina, Panzenboeck, Lisa, Gregor, Rachel, O’Neill, Ellis Charles, Roxborough, Eve Tallulah, Odoi, Jane, Bale, Nicole J., Ding, Su, Sinninghe Damsté, Jaap S., Guan, Xue Li, Cui, Jerry J., Ju, Kou San, Silva, Denise Brentan, Silva, Fernanda Motta Ribeiro, da Silva, Gilvan Ferreira, Koolen, Hector H.F., Grundmann, Carlismari, Clement, Jason A., Mohimani, Hosein, Broders, Kirk, McPhail, Kerry L., Ober-Singleton, Sidnee E., Rath, Christopher M., McDonald, Daniel, Knight, Rob, Wang, Mingxun, Dorrestein, Pieter C., Zuffa, Simone, Schmid, Robin, Bauermeister, Anelize, Paulo, Paulo Wender, Caraballo-Rodriguez, Andres M., El Abiead, Yasin, Aron, Allegra T., Gentry, Emily C., Zemlin, Jasmine, Meehan, Michael J., Avalon, Nicole E., Cichewicz, Robert H., Buzun, Ekaterina, Terrazas, Marvic Carrillo, Hsu, Chia Yun, Oles, Renee, Ayala, Adriana Vasquez, Zhao, Jiaqi, Chu, Hiutung, Kuijpers, Mirte C.M., Jackrel, Sara L., Tugizimana, Fidele, Nephali, Lerato Pertunia, Dubery, Ian A., Madala, Ntakadzeni Edwin, Moreira, Eduarda Antunes, Costa-Lotufo, Leticia Veras, Lopes, Norberto Peporine, Rezende-Teixeira, Paula, Jimenez, Paula C., Rimal, Bipin, Patterson, Andrew D., Traxler, Matthew F., Pessotti, Rita de Cassia, Alvarado-Villalobos, Daniel, Tamayo-Castillo, Giselle, Chaverri, Priscila, Escudero-Leyva, Efrain, Quiros-Guerrero, Luis Manuel, Bory, Alexandre Jean, Joubert, Juliette, Rutz, Adriano, Wolfender, Jean-Luc, Allard, Pierre-Marie, Sichert, Andreas, Pontrelli, Sammy, Pullman, Benjamin S., Bandeira, Nuno, Gerwick, William H., Gindro, Katia, Massana-Codina, Josep, Wagner, Berenike C., Forchhammer, Karl, Petras, Daniel, Aiosa, Nicole, Garg, Neha, Liebeke, Manuel, Bourceau, Patric, Kang, Kyo Bin, Gadhavi, Henna, de Carvalho, Luiz Pedro Sorio, Silva dos Santos, Mariana, Pérez-Lorente, Alicia Isabel, Molina-Santiago, Carlos, Romero, Diego, Franke, Raimo, Brönstrup, Mark, Vera Ponce de León, Arturo, Pope, Phillip Byron, La Rosa, Sabina Leanti, La Barbera, Giorgia, Roager, Henrik M., Laursen, Martin Frederik, Hammerle, Fabian, Siewert, Bianka, Peintner, Ursula, Licona-Cassani, Cuauhtemoc, Rodriguez-Orduña, Lorena, Rampler, Evelyn, Hildebrand, Felina, Koellensperger, Gunda, Schoeny, Harald, Hohenwallner, Katharina, Panzenboeck, Lisa, Gregor, Rachel, O’Neill, Ellis Charles, Roxborough, Eve Tallulah, Odoi, Jane, Bale, Nicole J., Ding, Su, Sinninghe Damsté, Jaap S., Guan, Xue Li, Cui, Jerry J., Ju, Kou San, Silva, Denise Brentan, Silva, Fernanda Motta Ribeiro, da Silva, Gilvan Ferreira, Koolen, Hector H.F., Grundmann, Carlismari, Clement, Jason A., Mohimani, Hosein, Broders, Kirk, McPhail, Kerry L., Ober-Singleton, Sidnee E., Rath, Christopher M., McDonald, Daniel, Knight, Rob, Wang, Mingxun, and Dorrestein, Pieter C.

Abstract

microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbe-derived metabolites and relative producers without a priori knowledge will vastly enhance the understanding of microorganisms’ role in ecology and human health.

Published
2024

8. Effects of Early Life Exposures to the Aryl Hydrocarbon Receptor Ligand TCDF on Gut Microbiota and Host Metabolic Homeostasis in C57BL/6J Mice.

Author

Yuan Tian, Rimal, Bipin, Bisanz, Jordan E., Wei Gui, Wolfe, Trenton M., Imhoi Koo, Murray, Iain A., Nettleford, Shaneice K., Shigetoshi Yokoyama, Fangcong Dong, Sergei Koshkin, Prabhu, K. Sandeep, Turnbaugh, Peter J., Walk, Seth T., Perdew, Gary H., and Patterson, Andrew D.

Subjects
*RNA analysis, *FECAL analysis, *DNA analysis, *IN vitro studies, *FLOW cytometry, *HIGH performance liquid chromatography, *HOMEOSTASIS, *RESEARCH funding, *GENOMICS, *NUCLEAR magnetic resonance spectroscopy, *SHORT-chain fatty acids, *T-test (Statistics), *STATISTICAL hypothesis testing, *HYDROCARBONS, *GUT microbiome, *GLUCAGON-like peptide 1, *GLUCOSE tolerance tests, *POLYMERASE chain reaction, *IN vivo studies, *DESCRIPTIVE statistics, *MANN Whitney U Test, *MICE, *PEPTIDES, *CELL culture, *IMMUNOHISTOCHEMISTRY, *POLLUTANTS, *ENVIRONMENTAL exposure, *ANIMAL experimentation, *MASS spectrometry, *GENE expression profiling, *LIPOPOLYSACCHARIDES, *ANALYSIS of variance, *METABOLOMICS, *BIOLOGICAL assay, *LACTIC acid, *STAINS & staining (Microscopy), *CYTOKINES, *TRIGLYCERIDES, *LIVER, *CONFIDENCE intervals, *DATA analysis software
Abstract

BACKGROUND: Exposure to persistent organic pollutants (POPs) and disruptions in the gastrointestinal microbiota have been positively correlated with a predisposition to factors such as obesity, metabolic syndrome, and type 2 diabetes; however, it is unclear how the microbiome contributes to this relationship. OBJECTIVE: This study aimed to explore the association between early life exposure to a potent aryl hydrocarbon receptor (AHR) agonist and persistent disruptions in the microbiota, leading to impaired metabolic homeostasis later in life. METHODS: This study used metagenomics, nuclear magnetic resonance (NMR)– and mass spectrometry (MS)–based metabolomics, and biochemical assays to analyze the gut microbiome composition and function, as well as the physiological and metabolic effects of early life exposure to 2,3,7,8-tetrachlorodibenzofuran (TCDF) in conventional, germ-free (GF), and Ahr-null mice. The impact of TCDF on Akkermansia muciniphila (A. muciniphila) in vitro was assessed using optical density (OD 600), flowcytometry, transcriptomics, and MS-based metabolomics. RESULTS: TCDF-exposed mice exhibited lower abundances of A. muciniphila, lower levels of cecal short-chain fatty acids (SCFAs) and indole-3- lactic acid (ILA), as well as lower levels of the gut hormones glucagon-like peptide 1 (GLP-1) and peptide YY (PYY), findings suggestive of disruption in the gut microbiome community structure and function. Importantly, microbial and metabolic phenotypes associated with early life POP exposure were transferable to GF recipients in the absence of POP carry-over. In addition, AHR-independent interactions between POPs and the microbiota were observed, and they were significantly associated with growth, physiology, gene expression, and metabolic activity outcomes of A. muciniphila, supporting suppressed activity along the ILA pathway. CONCLUSIONS: These data obtained in a mouse model point to the complex effects of POPs on the host and microbiota, providing strong evidence that early life, short-term, and self-limiting POP exposure can adversely impact the microbiome, with effects persisting into later life with associated health implications. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

11. Gut microbiota and intestinal FXR mediate the clinical benefits of metformin

Author

Sun, Lulu, Xie, Cen, Wang, Guang, Wu, Yue, Wu, Qing, Wang, Xuemei, Liu, Jia, Deng, Yangyang, Xia, Jialin, Chen, Bo, Zhang, Songyang, Yun, Chuyu, Lian, Guan, Zhang, Xiujuan, Zhang, Heng, Bisson, William H., Shi, Jingmin, Gao, Xiaoxia, Ge, Pupu, Liu, Cuihua, Krausz, Kristopher W., Nichols, Robert G., Cai, Jingwei, Rimal, Bipin, Patterson, Andrew D., Wang, Xian, Gonzalez, Frank J., and Jiang, Changtao

Published
2018
Full Text
View/download PDF

12. A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data

Author

Dorrestein, Pieter, primary, Zuffa, Simone, additional, Schmid, Robin, additional, Bauermeister, Anelize, additional, Gomes, Paulo Wender Portal, additional, Caraballo-Rodriguez, Andres, additional, Abiead, Yasin El, additional, Aron, Allegra, additional, Gentry, Emily, additional, Zemlin, Jasmine, additional, Meehan, Michael, additional, Avalon, Nicole, additional, Cichewicz, Robert, additional, Buzun, Ekaterina, additional, Carrillo-Terrazas, Marvic, additional, Hsu, Chia-Yun, additional, Oles, Renee, additional, Ayala, Adriana Vasquez, additional, Zhao, Jiaqi, additional, Chu, Hiutung, additional, Kuijpers, Mirte, additional, Jackrel, Sara, additional, Tugizimana, Fidele, additional, Nephali, Lerato, additional, Dubery, Ian, additional, Madala, Ntakadzeni, additional, Moreira, Eduarda, additional, Costa-Lotufo, Leticia, additional, Lopes, Norberto, additional, Rezende-Teixeira, Paula, additional, Jimenez, Paula, additional, Rimal, Bipin, additional, Patterson, Andrew, additional, Traxler, Matthew, additional, Pessotti, Rita de Cassia, additional, Alvarado-Villalobos, Daniel, additional, Tamayo-Castillo, Giselle, additional, Chaverri, Priscila, additional, Escudero-Leyva, Efrain, additional, Quiros-Guerrero, Luis-Manuel, additional, Bory, Alexandre, additional, Joubert, Juliette, additional, Rutz, Adriano, additional, Wolfender, Jean-Luc, additional, Allard, Pierre-Marie, additional, Sichert, Andreas, additional, Pontrelli, Sammy, additional, Pullman, Benjamin, additional, Bandeira, Nuno, additional, Gerwick, William, additional, Gindro, Katia, additional, Massana-Codina, Josep, additional, Wagner, Berenike, additional, Forchhammer, Karl, additional, Petras, Daniel, additional, Aiosa, Nicole, additional, Garg, Neha, additional, Liebeke, Manuel, additional, Bourceau, Patric, additional, Kang, Kyo Bin, additional, Gadhavi, Henna, additional, de Carvalho, Luiz Pedro, additional, Santos, Mariana Silva dos, additional, Pérez-Lorente, Alicia, additional, Molina-Santiago, Carlos, additional, Romero, Diego, additional, Franke, Raimo, additional, Broenstrup, Mark, additional, De Leon, Arturo Vera Ponce, additional, Pope, Phillip, additional, Rosa, Sabina La, additional, Barbera, Giorgia La, additional, Roager, Henrik, additional, Laursen, Martin, additional, Hammerle, Fabian, additional, Siewert, Bianka, additional, Peintner, Ursula, additional, Licona-Cassani, Cuauhtemoc, additional, Rodriguez-Orduña, Lorena, additional, Rampler, Evelyn, additional, Hildebrand, Felina, additional, Koellensperger, Gunda, additional, Schoeny, Harald, additional, Hohenwallner, Katharina, additional, Panzenboeck, Lisa, additional, Gregor, Rachel, additional, O'Neill, Ellis, additional, Roxborough, Eve, additional, Odoi, Jane, additional, Bale, Nicole, additional, Ding, Su, additional, Damsté, Jaap S. Sinninghe, additional, Guan, Xueli, additional, Cui, Jerry, additional, Ju, Kou-San, additional, Silva, Denise, additional, Silva, Fernanda, additional, Silva, Gilvan da, additional, Koolen, Hector, additional, Grundmann, Carlismari, additional, Clement, Jason, additional, Mohimani, Hosein, additional, Broders, Kirk, additional, McPhail, Kerry, additional, Ober-Singleton, Sidnee, additional, Rath, Christopher, additional, McDonald, Daniel, additional, Knight, Rob, additional, and Wang, Mingxun, additional

Published
2023
Full Text
View/download PDF

13. A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data

Author

Zuffa, Simone, primary, Schmid, Robin, additional, Bauermeister, Anelize, additional, Gomes, Paulo Wender P., additional, Caraballo-Rodriguez, Andres M., additional, Abiead, Yasin El, additional, Aron, Allegra T., additional, Gentry, Emily C., additional, Zemlin, Jasmine, additional, Meehan, Michael J., additional, Avalon, Nicole E., additional, Cichewicz, Robert H., additional, Buzun, Ekaterina, additional, Terrazas, Marvic Carrillo, additional, Hsu, Chia-Yun, additional, Oles, Renee, additional, Ayala, Adriana Vasquez, additional, Zhao, Jiaqi, additional, Chu, Hiutung, additional, Kuijpers, Mirte C. M., additional, Jackrel, Sara L., additional, Tugizimana, Fidele, additional, Nephali, Lerato Pertunia, additional, Dubery, Ian A., additional, Madala, Ntakadzeni Edwin, additional, Moreira, Eduarda Antunes, additional, Costa-Lotufo, Leticia Veras, additional, Lopes, Norberto Peporine, additional, Rezende-Teixeira, Paula, additional, Jimenez, Paula C., additional, Rimal, Bipin, additional, Patterson, Andrew D., additional, Traxler, Matthew F., additional, de Cassia Pessotti, Rita, additional, Alvarado-Villalobos, Daniel, additional, Tamayo-Castillo, Giselle, additional, Chaverri, Priscila, additional, Escudero-Leyva, Efrain, additional, Quiros-Guerrero, Luis-Manuel, additional, Bory, Alexandre Jean, additional, Joubert, Juliette, additional, Rutz, Adriano, additional, Wolfender, Jean-Luc, additional, Allard, Pierre-Marie, additional, Sichert, Andreas, additional, Pontrelli, Sammy, additional, Pullman, Benjamin S, additional, Bandeira, Nuno, additional, Gerwick, William H., additional, Gindro, Katia, additional, Massana-Codina, Josep, additional, Wagner, Berenike C., additional, Forchhammer, Karl, additional, Petras, Daniel, additional, Aiosa, Nicole, additional, Garg, Neha, additional, Liebeke, Manuel, additional, Bourceau, Patric, additional, Kang, Kyo Bin, additional, Gadhavi, Henna, additional, de Carvalho, Luiz Pedro Sorio, additional, dos Santos, Mariana Silva, additional, Pérez-Lorente, Alicia Isabel, additional, Molina-Santiago, Carlos, additional, Romero, Diego, additional, Franke, Raimo, additional, Brönstrup, Mark, additional, de León, Arturo Vera Ponce, additional, Pope, Phillip Byron, additional, La Rosa, Sabina Leanti, additional, Barbera, Giorgia La, additional, Roager, Henrik M., additional, Laursen, Martin Frederik, additional, Hammerle, Fabian, additional, Siewert, Bianka, additional, Peintner, Ursula, additional, Licona-Cassani, Cuauhtemoc, additional, Rodriguez-Orduña, Lorena, additional, Rampler, Evelyn, additional, Hildebrand, Felina, additional, Koellensperger, Gunda, additional, Schoeny, Harald, additional, Hohenwallner, Katharina, additional, Panzenboeck, Lisa, additional, Gregor, Rachel, additional, O’Neill, Ellis Charles, additional, Roxborough, Eve Tallulah, additional, Odoi, Jane, additional, Bale, Nicole J., additional, Ding, Su, additional, Sinninghe Damsté, Jaap S., additional, Guan, Xueli Li, additional, Cui, Jerry J., additional, Ju, Kou-San, additional, Silva, Denise Brentan, additional, Ribeiro Silva, Fernanda Motta, additional, da Silva, Gilvan Ferreira, additional, Koolen, Hector H. F., additional, Grundmann, Carlismari, additional, Clement, Jason A., additional, Mohimani, Hosein, additional, Broders, Kirk, additional, McPhail, Kerry L., additional, Ober-Singleton, Sidnee E., additional, Rath, Christopher M., additional, McDonald, Daniel, additional, Knight, Rob, additional, Wang, Mingxun, additional, and Dorrestein, Pieter C., additional

Published
2023
Full Text
View/download PDF

14. Early-life exposure to a potent Aryl hydrocarbon receptor ligand results in persistent changes to the microbiota and host glucose homeostasis

Author

Tian, Yuan, primary, Rimal, Bipin, additional, Bisanz, Jordan E., additional, Gui, Wei, additional, Wolfe, Trenton M., additional, Koo, Imhoi, additional, Murray, Iain M., additional, Nettleford, Shaneice K., additional, Yokoyama, Shigetoshi, additional, Dong, Fangcong, additional, Prabhu, K. Sandeep, additional, Turnbaugh, Peter J., additional, Walk, Seth T., additional, Perdew, Gary H., additional, and Patterson, Andrew D., additional

Published
2023
Full Text
View/download PDF

16. BSH_resubmission

Author

Rimal, Bipin, Collins, Stephanie L., and Patterson, Andrew D.

Abstract

Data, and codes to generate figures in BSH resubmission

Published
2023
Full Text
View/download PDF

17. BSH_CRC_lulu et al

Author

Sun, Lulu, Rimal, Bipin, and Gonzalez, Frank

Abstract

Role of non-toxigenic bacteroides fragilis bile acid hydrolase in colorectal cancer: - Codes for metagenomics data analysis for functional profiling - Codes for bile salt hydrolase abundance

Published
2022
Full Text
View/download PDF

18. Utilization of 16s sequencing data and physiological measurements to produce a comparative analysis of the equine microbiome.

Author

Jacobs, Robert D., Rimal, Bipin, Lahoti, Manohar M., Bowman, Morghan, and Gordon, Mary Beth

Subjects
*BACTERIAL ecology, *MICROBIAL ecology, *SOIL microbiology, *BACTERIAL population, *HORSE health, *HORSE breeding
Abstract

Rapid advancements in microbiome research, particularly in the technologies associated with nextgeneration sequencing have enabled unprecedented investigations into the composition of the equine microbiome. The large datasets produced from these studies often present challenges to researchers seeking to understand the applicability of these data to equine physiology. To that end, a multi-year project was conducted with the goal of determining the core bacterial population of the equine hindgut through analysis of rectal swabs collected from thousands of horses and applying logic to the association between these ecologies and equine health. Samples were obtained from horses that varied across a diverse range of considerations including location, breed, age, and diet, amongst other metadata points including disease state, health history, vaccination and deworming status, body condition, and pregnancy status. These data were used in the development of a comparative score, that authors defined as the Microbiome Quotient (MQ score). Rectal swabs were collected, and DNA was extracted using the Quick-DNA Fecal/Soil Microbe Miniprep kit (Zymo Research, Irvine, CA) and the V3-V4 hypervariable region of the 16S rRNA gene was sequenced by following the Illumina 16S Protocol (San Diego, CA). Sequences were denoised using DADA2 within the QIIME2 pipeline to obtain amplicon sequence variant composition. These data were filtered again in R (4.2.2) to remove samples with missing data and low sequencing depth. Sample metadata was used to classify samples as either typical or atypical. The MQ score was calculated by computing the Euclidean distance difference between a sample and the centroids representing typical and atypical microbial ecologies, and then subtracting these distances to obtain the individual score. This score quantifies how similar the microbiome in a sample is to those of typical and atypical horses. These scores were then categorized into tertiles, representing the status of the individual horse’s microbiome. These statuses indicate differences in bacterial ecology among samples and their subsequent relevance to the health of the horse. While a large portion of the equine fecal microbiome is conserved through homeostatic and other mechanisms, there remains a high degree of variability in the lesser abundant genera that may be responsible for the different physiological interactions between the microbes and their hosts. Utilizing this MQ score, feeding and management recommendations can be made, providing veterinarians and horse owners with a tool to support the health and performance of horses through modulation of the bacterial population and its functionality. Further research is necessary to fully elucidate the impact of the various metadata components on the bacterial ecology. Additionally, the function of the metagenome is a critical component of microbiome sciences. Prediction of metagenomic function is likely to provide insight into the regulation of physiological function by the microbial population residing within the host. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

20. Bile Acids Are Substrates for Amine N-Acyl Transferase Activity by Bile Salt Hydrolase

Author

Patterson, Andrew, primary, Rimal, Bipin, additional, Collins, Stephanie, additional, Granda, Megan, additional, Koo, Imhoi, additional, Solanka, Sumeet, additional, Hoque, Nushrat, additional, Gentry, Emily, additional, Yan, Tingting, additional, Bisanz, Jordan, additional, Krausz, Kristopher, additional, Desai, Dhimant, additional, Amin, Shantu, additional, Rocha, Edson, additional, Coleman, James, additional, Shah, Yatrik, additional, Gonzalez, Frank, additional, Heuvel, John Vanden, additional, Dorrestein, Pieter, additional, and Weinert, Emily, additional

Published
2022
Full Text
View/download PDF

24. Bile acid conjugation deficiency causes hypercholanemia, hyperphagia, islet dysfunction, and gut dysbiosis in mice

Author

Alrehaili, Bandar D., primary, Lee, Mikang, additional, Takahashi, Shogo, additional, Novak, Robert, additional, Rimal, Bipin, additional, Boehme, Shannon, additional, Trammell, Samuel A. J., additional, Grevengoed, Trisha J., additional, Kumar, Devendra, additional, Alnouti, Yazen, additional, Chiti, Katya, additional, Wang, Xinwen, additional, Patterson, Andrew D., additional, Chiang, John Y. L., additional, Gonzalez, Frank J., additional, and Lee, Yoon‐Kwang, additional

Published
2022
Full Text
View/download PDF

25. Bile acid conjugation deficiency causes hypercholanemia, hyperphagia, islet dysfunction, and gut dysbiosis in mice

Author

Alrehaili, Bandar D., Lee, Mikang, Takahashi, Shogo, Novak, Robert, Rimal, Bipin, Boehme, Shannon, Trammell, Samuel A. J., Grevengoed, Trisha J., Kumar, Devendra, Alnouti, Yazen, Chiti, Katya, Wang, Xinwen, Patterson, Andrew D., Chiang, John Y. L., Gonzalez, Frank J., Lee, Yoon-Kwang, Alrehaili, Bandar D., Lee, Mikang, Takahashi, Shogo, Novak, Robert, Rimal, Bipin, Boehme, Shannon, Trammell, Samuel A. J., Grevengoed, Trisha J., Kumar, Devendra, Alnouti, Yazen, Chiti, Katya, Wang, Xinwen, Patterson, Andrew D., Chiang, John Y. L., Gonzalez, Frank J., and Lee, Yoon-Kwang

Abstract

Bile acid-CoA: amino acid N-acyltransferase (BAAT) catalyzes bile acid conjugation, the last step in bile acid synthesis. BAAT gene mutation in humans results in hypercholanemia, growth retardation, and fat-soluble vitamin insufficiency. The current study investigated the physiological function of BAAT in bile acid and lipid metabolism using Baat(-/-) mice. The bile acid composition and hepatic gene expression were analyzed in 10-week-old Baat(-/-) mice. They were also challenged with a westernized diet (WD) for additional 15 weeks to assess the role of BAAT in bile acid, lipid, and glucose metabolism. Comprehensive lab animal monitoring system and cecal 16S ribosomal RNA gene sequencing were used to evaluate the energy metabolism and microbiome structure of the mice, respectively. In Baat(-/-) mice, hepatic bile acids were mostly unconjugated and their levels were significantly increased compared with wild-type mice. Bile acid polyhydroxylation was markedly up-regulated to detoxify unconjugated bile acid accumulated in Baat(-/-) mice. Although the level of serum marker of bile acid synthesis, 7 alpha-hydroxy-4-cholesten-3-one, was higher in Baat(-/-) mice, their bile acid pool size was smaller. When fed a WD, the Baat(-/-) mice showed a compromised body weight gain and impaired insulin secretion. The gut microbiome of Baat(-/-) mice showed a low level of sulfidogenic bacteria Bilophila. Conclusion: Mouse BAAT is the major taurine-conjugating enzyme. Its deletion protected the animals from diet-induced obesity, but caused glucose intolerance. The gut microbiome of the Baat(-/-) mice was altered to accommodate the unconjugated bile acid pool.

Published
2022

27. The microbiome modulating activity of bile acids

Author

Tian, Yuan, primary, Gui, Wei, additional, Koo, Imhoi, additional, Smith, Philip B., additional, Allman, Erik L., additional, Nichols, Robert G., additional, Rimal, Bipin, additional, Cai, Jingwei, additional, Liu, Qing, additional, and Patterson, Andrew D., additional

Published
2020
Full Text
View/download PDF

29. Prevalence of Bovine Tuberculosis in India: A systematic review and meta-analysis

Author

Srinivasan, Sreenidhi, Easterling, Laurel, Rimal, Bipin, Niu, Xiaoyue Maggie, Conlan, Andrew JK, Dudas, Patrick, Kapur, Vivek, Easterling, Laurel [0000-0002-1122-0696], and Apollo - University of Cambridge Repository

Subjects
Buffaloes, prevalence, review, India, Breeding, meta-analysis, cows, Cross-Sectional Studies, cattle, Animals, Humans, Female, Public Health, bovine tuberculosis, control program, Tuberculosis, Bovine
Abstract

Bovine tuberculosis (bTB) is a chronic disease of cattle that impacts productivity and represents a major public health threat. Despite the considerable economic costs and zoonotic risk consequences associated with the disease, accurate estimates of bTB prevalence are lacking in many countries, including India, where national control programmes are not yet implemented and the disease is considered endemic. To address this critical knowledge gap, we performed a systematic review of the literature and a meta-analysis to estimate bTB prevalence in cattle in India and provide a foundation for the future formulation of rational disease control strategies and the accurate assessment of economic and health impact risks. The literature search was performed in accordance with PRISMA guidelines and identified 285 cross-sectional studies on bTB in cattle in India across four electronic databases and handpicked publications. Of these, 44 articles were included, contributing a total of 82,419 cows and buffaloes across 18 states and one union territory in India. Based on a random-effects (RE) meta-regression model, the analysis revealed a pooled prevalence estimate of 7.3% (95% CI: 5.6, 9.5), indicating that there may be an estimated 21.8 million (95% CI: 16.6, 28.4) infected cattle in India-a population greater than the total number of dairy cows in the United States. The analyses further suggest that production system, species, breed, study location, diagnostic technique, sample size and study period are likely moderators of bTB prevalence in India and need to be considered when developing future disease surveillance and control programmes. Taken together with the projected increase in intensification of dairy production and the subsequent increase in the likelihood of zoonotic transmission, the results of our study suggest that attempts to eliminate tuberculosis from humans will require simultaneous consideration of bTB control in cattle population in countries such as India.

Published
2018
Full Text
View/download PDF

32. A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data.

Author

Zuffa S, Schmid R, Bauermeister A, Gomes PWP, Caraballo-Rodriguez AM, Abiead YE, Aron AT, Gentry EC, Zemlin J, Meehan MJ, Avalon NE, Cichewicz RH, Buzun E, Terrazas MC, Hsu CY, Oles R, Ayala AV, Zhao J, Chu H, Kuijpers MCM, Jackrel SL, Tugizimana F, Nephali LP, Dubery IA, Madala NE, Moreira EA, Costa-Lotufo LV, Lopes NP, Rezende-Teixeira P, Jimenez PC, Rimal B, Patterson AD, Traxler MF, de Cassia Pessotti R, Alvarado-Villalobos D, Tamayo-Castillo G, Chaverri P, Escudero-Leyva E, Quiros-Guerrero LM, Bory AJ, Joubert J, Rutz A, Wolfender JL, Allard PM, Sichert A, Pontrelli S, Pullman BS, Bandeira N, Gerwick WH, Gindro K, Massana-Codina J, Wagner BC, Forchhammer K, Petras D, Aiosa N, Garg N, Liebeke M, Bourceau P, Kang KB, Gadhavi H, de Carvalho LPS, Dos Santos MS, Pérez-Lorente AI, Molina-Santiago C, Romero D, Franke R, Brönstrup M, de León AVP, Pope PB, Rosa SL, Barbera G, Roager HM, Laursen MF, Hammerle F, Siewert B, Peintner U, Licona-Cassani C, Rodriguez-Orduña L, Rampler E, Hildebrand F, Koellensperger G, Schoeny H, Hohenwallner K, Panzenboeck L, Gregor R, O'Neill EC, Roxborough ET, Odoi J, Bale NJ, Ding S, Sinninghe Damsté JS, Guan XL, Cui JJ, Ju KS, Silva DB, Silva FMR, da Silva GF, Koolen HHF, Grundmann C, Clement JA, Mohimani H, Broders K, McPhail KL, Ober-Singleton SE, Rath CM, McDonald D, Knight R, Wang M, and Dorrestein PC

Abstract

MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbial-derived metabolites and relative producers, without a priori knowledge, will vastly enhance the understanding of microorganisms' role in ecology and human health., Competing Interests: Disclosures PCD is an advisor to Cybele, consulted for MSD animal health in 2023, and he is a Co-founder and scientific advisor for Ometa Labs, Arome, and Enveda with prior approval by UC San Diego. MW is a Co-founder of Ometa labs. There are no known conflicts of interest in this work by the USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture.

Published
2023
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results