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7. High Persistence of Novel Polyfluoroalkyl Betaines in Aerobic Soils

Author

Liu, Min, primary, Munoz, Gabriel, additional, Hermiston, Juliana, additional, Zhang, Ju, additional, Vo Duy, Sung, additional, Wang, Dan, additional, Sundar Dey, Anindya, additional, Bottos, Eric M., additional, Van Hamme, Jonathan D., additional, Lee, Linda S., additional, Sauvé, Sébastien, additional, and Liu, Jinxia, additional

Published
2023
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11. Accumulation of Black Carbon Particles in Placenta, Cord Blood, and Childhood Urine in Association with the Intestinal Microbiome Diversity and Composition in Four- to Six-Year-Old Children in the ENVIR ON AGE Birth Cohort

Author

Van Pee, Thessa, primary, Hogervorst, Janneke, additional, Dockx, Yinthe, additional, Witters, Katrien, additional, Thijs, Sofie, additional, Wang, Congrong, additional, Bongaerts, Eva, additional, Van Hamme, Jonathan D., additional, Vangronsveld, Jaco, additional, Ameloot, Marcel, additional, Raes, Jeroen, additional, and Nawrot, Tim S., additional

Published
2023
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13. Subsurface Petroleum Microbiology

Author

Singh, Ajay, Van Hamme, Jonathan D., Kuhad, Ramesh C., Parmar, Nagina, Ward, Owen P., Varma, Ajit, Series editor, Parmar, Nagina, editor, and Singh, Ajay, editor

Published
2014
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18. Accumulation of Black Carbon Particles in Placenta, Cord Blood, and Childhood Urine in Association with the Intestinal Microbiome Diversity and Composition in Four- to Six-Year-Old Children in the ENVIRONAGE Birth Cohort.

Author

Van Pee, Thessa, Hogervorst, Janneke, Dockx, Yinthe, Witters, Katrien, Thijs, Sofie, Congrong Wang, Bongaerts, Eva, Van Hamme, Jonathan D., Vangronsveld, Jaco, Ameloot, Marcel, Raes, Jeroen, and Nawrot, Tim S.

Subjects
RNA analysis, FECAL analysis, CARBON analysis, AIR pollution, PARTICULATE matter, STATISTICS, LIFESTYLES, MOTHERS, CONFIDENCE intervals, SEQUENCE analysis, GUT microbiome, MULTIVARIATE analysis, MULTIPLE regression analysis, PRENATAL exposure delayed effects, CORD blood, SOCIOECONOMIC factors, ENVIRONMENTAL health, PLACENTA, RESEARCH funding, DESCRIPTIVE statistics, URINALYSIS, DATA analysis software, DATA analysis, PREGNANCY
Abstract

BACKGROUND: The gut microbiome plays an essential role in human health. Despite the link between air pollution exposure and various diseases, its association with the gut microbiome during susceptible life periods remains scarce. OBJECTIVES: In this study, we examined the association between black carbon particles quantified in prenatal and postnatal biological matrices and bacterial richness and diversity measures, and bacterial families. METHODS: A total of 85 stool samples were collected from 4- to 6-y-old children enrolled in the ENVIRonmental influence ON early AGEing birth cohort. We performed 16S rRNA gene sequencing to calculate bacterial richness and diversity indices (Chao1 richness, Shannon diversity, and Simpson diversity) and the relative abundance of bacterial families. Black carbon particles were quantified via white light generation under femtosecond pulsed laser illumination in placental tissue and cord blood, employed as prenatal exposure biomarkers, and in urine, used as a post-natal exposure biomarker. We used robust multivariable-adjusted linear models to examine the associations between quantified black carbon loads and measures of richness (Chao1 index) and diversity (Shannon and Simpson indices), adjusting for parity, season of delivery, sequencing batch, age, sex, weight and height of the child, and maternal education. Additionally, we performed a differential relative abundance analysis of bacterial families with a correction for sampling fraction bias. Results are expressed as percentage difference for a doubling in black carbon loads with 95% confidence interval (CI). RESULTS: Two diversity indices were negatively associated with placental black carbon [Shannon: -4.38% (95% CI: -8.31%, -0.28%); Simpson: -0.90% (95% CI: -1.76%, -0.04%)], cord blood black carbon [Shannon: -3.38% (95% CI: -5.66%, -0:84%); Simpson: -0.91 (95% CI: -1.66%, -0.16%)], and urinary black carbon [Shannon: -3.39% (95% CI: -5.77%, -0.94%); Simpson: -0.89% (95% CI: -1.37%, -0.40%)]. The explained variance of black carbon on the above indices varied from 6.1% to 16.6%. No statistically significant associations were found between black carbon load and the Chao1 richness index. After multiple testing correction, placental black carbon was negatively associated with relative abundance of the bacterial families Defluviitaleaceae and Marinifilaceae, and urinary black carbon with Christensenellaceae and Coriobacteriaceae; associations with cord blood black carbon were not statistically significant after correction. CONCLUSION: Black carbon particles quantified in prenatal and postnatal biological matrices were associated with the composition and diversity of the childhood intestinal microbiome. These findings address the influential role of exposure to air pollution during pregnancy and early life in human health. [ABSTRACT FROM AUTHOR]

Published
2023
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25. Correlation of Breed, Growth Performance, and Rumen Microbiota in Two Rustic Cattle Breeds Reared Under Different Conditions

Author

Daghio, Matteo, primary, Ciucci, Francesca, additional, Buccioni, Arianna, additional, Cappucci, Alice, additional, Casarosa, Laura, additional, Serra, Andrea, additional, Conte, Giuseppe, additional, Viti, Carlo, additional, McAmmond, Breanne M., additional, Van Hamme, Jonathan D., additional, and Mele, Marcello, additional

Published
2021
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26. Effluent decontamination by the ibuprofen-mineralizing strain, Sphingopyxis granuli RW412: Metabolic processes

Author

Aguilar-Romero, Inés, primary, De la Torre-Zúñiga, Jesús, additional, Quesada, José Miguel, additional, Haïdour, Ali, additional, O’Connell, Garret, additional, McAmmond, Breanne M., additional, Van Hamme, Jonathan D., additional, Romero, Esperanza, additional, Wittich, Regina-Michaela, additional, and van Dillewijn, Pieter, additional

Published
2021
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28. Isolation, Biochemical and Genomic Characterization of Glyphosate Tolerant Bacteria to Perform Microbe-Assisted Phytoremediation

Author

Massot, Francisco, primary, Gkorezis, Panagiotis, additional, Van Hamme, Jonathan, additional, Marino, Damian, additional, Trifunovic, Bojana Spirovic, additional, Vukovic, Gorica, additional, d’Haen, Jan, additional, Pintelon, Isabel, additional, Giulietti, Ana María, additional, Merini, Luciano, additional, Vangronsveld, Jaco, additional, and Thijs, Sofie, additional

Published
2021
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30. Physical and metabolic interactions of Pseudomonas sp. strain JA5-B45 and Rhodococcus sp. strain F9-D79 during growth on crude oil and effect of a chemical surfactant on them

Author

Van Hamme, Jonathan D. and Ward, Owen P.

Subjects
Biodegradation -- Research, Surface active agents -- Research, Petroleum -- Biodegradation, Biological sciences
Abstract

Adding a chemical surfactant to crude oil can enhance its biodegradation by Pseudomonas sp. strain JA5-B45 and Rhodococcus sp. strain F9-D79. The surfactant increases total petroleum hydrocarbon removal and keeps the bacteria from adhering to the oil-water interface.

Published
2001

31. Dissecting the cofactor-dependent and independent bindings of PDE4 inhibitors

Author

Liu, Susana, Laliberte, France, Bobechko, Brian, Bartlett, Adrienne, Lario, Paula, Gorseth, Elise, Van Hamme, Jonathan, Gresser, Michael J., and Huang, Zheng

Subjects
Biochemistry -- Research, Phosphodiesterases -- Physiological aspects, Hydrolysis -- Analysis, Dissection -- Analysis, Magnesium (Nutrient) -- Physiological aspects, Biological sciences, Chemistry
Abstract

Research has been conducted on the type 4 phosphodiesterase, a metallohydrolase catalyzing the hydrolysis of cAMP to AMP. The dissecting of the cofactor-dependent and independent binding of the inhibitors and the catalytic activity of the type 4 phosphodiesterase has been investigated via the developed [(super)3 H]rolipram equilibrium-based binding assay.

Published
2001

37. Enzyme Catalyzed Formation of CoA Adducts of Fluorinated Hexanoic Acid Analogues using a Long-Chain acyl-CoA Synthetase from Gordoniasp. Strain NB4-1Y

Author

Mothersole, Robert G., Mothersole, Mina K., Goddard, Hannah G., Liu, Jinxia, and Van Hamme, Jonathan D.

Abstract

Per and polyfluoroalkyl substances (PFAS) are a large family of anthropogenic fluorinated chemicals of increasing environmental concern. Over recent years, numerous microbial communities have been found to be capable of metabolizing some polyfluoroalkyl substances, generating a range of low-molecular-weight PFAS metabolites. One proposed pathway for the microbial breakdown of fluorinated carboxylates includes β-oxidation, this pathway is initiated by the formation of a CoA adduct. However, until recently no PFAS-CoA adducts had been reported. In a previous study, we were able to use a bacterial medium-chain acyl-CoA synthetase (mACS) to form CoA adducts of fluorinated adducts of propanoic acid and pentanoic acid but were not able to detect any products of fluorinated hexanoic acid analogues. Herein, we expressed and purified a long-chain acyl-CoA synthetase (lACS) and a A461K variant of mACS from the soil bacterium Gordoniasp. strain NB4–1Y and performed an analysis of substrate scope and enzyme kinetics using fluorinated and nonfluorinated carboxylates. We determined that lACS can catalyze the formation of CoA adducts of 1:5 fluorotelomer carboxylic acid (FTCA), 2:4 FTCA and 3:3 FTCA, albeit with generally low turnover rates (<0.02 s–1) compared with the nonfluorinated hexanoic acid (5.39 s–1). In addition, the A461K variant was found to have an 8-fold increase in selectivity toward hexanoic acid compared with wild-type mACS, suggesting that Ala-461 has a mechanistic role in selectivity toward substrate chain length. This provides further evidence to validate the proposed activation step involving the formation of CoA adducts in the enzymatic breakdown of PFAS.

Published
2024
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41. Erratum: Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range

Author

Henderson, Gemma, Cox, Faith, Ganesh, Siva, Jonker, Arjan, Young, Wayne, Abecia, Leticia, Angarita, Erika, Aravena, Paula, Nora Arenas, Graciela, Ariza, Claudia, Attwood, Graeme T., Mauricio Avila, Jose, Avila-stagno, Jorge, Bannink, André, Barahona, Rolando, Batistotti, Mariano, Bertelsen, Mads F., Brown-Kav, Aya, Carvajal, Andres M., Cersosimo, Laura, Vieira Chaves, Alexandre, Church, John, Clipson, Nicholas, Cobos-peralta, Mario A., Cookson, Adrian L., Cravero, Silvio, Cristobal Carballo, Omar, Crosley, Katie, Cruz, Gustavo, Cerón Cucchi, María, de la Barra, Rodrigo, de Menezes, Alexandre B., Detmann, Edenio, Dieho, Kasper, Dijkstra, Jan, Dos Reis, William L.S., Dugan, Mike E.R., Hadi Ebrahimi, Seyed, Eythórsdóttir, Emma, Nde Fon, Fabian, Fraga, Martín, Franco, Francisco, Friedeman, Chris, Fukuma, Naoki, Gagić, Dragana, Gangnat, Isabelle, Javier Grilli, Diego, Guan, Le Luo, Heidarian Miri, Vahideh, Hernandez-Sanabria, Emma, Gomez, Alma Ximena Ibarra, Isah, Olubukola A., Ishaq, Suzanne, Jami, Elie, Jelincic, Juan, Kantanen, Juha, Kelly, William J., Kim, Seon-Ho, Klieve, Athol, Kobayashi, Yasuo, Koike, Satoshi, Kopecny, Jan, Nygaard Kristensen, Torsten, Julie Krizsan, Sophie, Lachance, Hannah, Lachman, Medora, Lamberson, William R., Lambie, Suzanne, Lassen, Jan, Leahy, Sinead C., Lee, Sang-Suk, Leiber, Florian, Lewis, Eva, Lin, Bo, Lira, Raúl, Lund, Peter, Macipe, Edgar, Mamuad, Lovelia L., Cuquetto Mantovani, Hilário, Marcoppido, Gisela Ariana, Márquez, Cristian, Martin, Cécile, Martinez, Gonzalo, Eugenia Martinez, Maria, Lucía Mayorga, Olga, McAllister, Tim A., McSweeney, Chris, Mestre, Lorena, Minnee, Elena, Mitsumori, Makoto, Mizrahi, Itzhak, Molina, Isabel, Muenger, Andreas, Muñoz, Camila, Murovec, Bostjan, Newbold, John, Nsereko, Victor, O’donovan, Michael, Okunade, Sunday, O’neill, Brendan, Ospina, Sonia, Ouwerkerk, Diane, Parra, Diana, Pereira, Luiz Gustavo Ribeiro, Pinares-patiño, Cesar, Pope, Phil B., Poulsen, Morten, Rodehutscord, Markus, Rodriguez, Tatiana, Saito, Kunihiko, Sales, Francisco, Sauer, Catherine, Shingfield, Kevin, Shoji, Noriaki, Simunek, Jiri, Stojanović-Radić, Zorica, Stres, Blaz, Sun, Xuezhao, Swartz, Jeffery, Liang Tan, Zhi, Tapio, Ilma, Taxis, Tasia M., Tomkins, Nigel, Ungerfeld, Emilio, Valizadeh, Reza, van Adrichem, Peter, van Hamme, Jonathan, van Hoven, Woulter, Waghorn, Garry, Wallace, John R., Wang, Min, Waters, Sinéad M., Keogh, Kate, Witzig, Maren, Wright, Andre-Denis G., Yamano, Hidehisa, Yan, Tianhai, Yáñez-ruiz, David R., Yeoman, Carl J., Zambrano, Ricardo, Zeitz, Johanna, Zhou, Mi, Wei Zhou, Hua, Xia Zou, Cai, Zunino, Pablo, and Janssen, Peter H.

Subjects
Multidisciplinary, Animal Nutrition, WIAS, Life Science, Laboratorium voor Plantenfysiologie, Diervoeding, Laboratory of Plant Physiology
Abstract

Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific.

Published
2016

42. The Interaction between Plants and Bacteria in the Remediation of Petroleum Hydrocarbons: An Environmental Perspective

Author

Gkorezis, Panagiotis, Daghio, Matte, Franzetti, Andrea, Van Hamme, Jonathan D., Sillen, Wouter, and Vangronsveld, Jaco

Subjects
phytoremediation, bioremediation, remediation, petroleum hydrocarbons, plant-bacteria assisted remediation, plant–bacteria assisted remediation
Abstract

Widespread pollution of terrestrial ecosystems with petroleum hydrocarbons (PHGs) has generated a need for remediation and, given that many PHCs are biodegradable, bio- and phyto-remediation are often viable approaches for active and passive remediation. This review focuses on phytoremediation with particular interest on the interactions between and use of plant-associated bacteria to restore PHC polluted sites. Plant-associated bacteria include endophytic, phyllospheric, and rhizospheric bacteria, and cooperation between these bacteria and their host plants allows for greater plant survivability and treatment outcomes in contaminated sites. Bacterially driven PHC bioremediation is attributed to the presence of diverse suites of metabolic genes for aliphatic and aromatic hydrocarbons, along with a broader suite of physiological properties including biosurfactant production, biofilm formation, chemotaxis to hydrocarbons, and flexibility in cell-surface hydrophobicity. In soils impacted by PHC contamination, microbial bioremediation generally relies on the addition of high-energy electron acceptors (e.g., oxygen) and fertilization to supply limiting nutrients (e.g., nitrogen, phosphorous, potassium) in the face of excess PHC carbon. As an alternative, the addition of plants can greatly improve bioremediation rates and outcomes as plants provide microbial habitats, improve soil porosity (thereby increasing mass transfer of substrates and electron acceptors), and exchange limiting nutrients with their microbial counterparts. In return, plant-associated microorganisms improve plant growth by reducing soil toxicity through contaminant removal, producing plant growth promoting metabolites, liberating sequestered plant nutrients from soil, fixing nitrogen, and more generally establishing the foundations of soil nutrient cycling. In a practical and applied sense, the collective action of plants and their associated microorganisms is advantageous for remediation of PHC contaminated soil in terms of overall cost and success rates for in situ implementation in a diversity of environments. Mechanistically, there remain biological unknowns that present challenges for applying bio- and phyto-remediation technologies without having a deep prior understanding of individual target sites. In this review, evidence from traditional and modern omics technologies is discussed to provide a framework for plant microbe interactions during PHC remediation. The potential for integrating multiple molecular and computational techniques to evaluate linkages between microbial communities, plant communities and ecosystem processes is explored with an eye on improving phytoremediation of PHC contaminated sites. This work was supported by the Hasselt University BOF project 06G02 and the Methusalem project 08M03VGRJ.

Published
2016

49. Use of a novel fluorinated organosulfur compound to isolate bacteria capable of carbon-sulfur bond cleavage

Author

Van Hamme, Jonathan D., Fedorak, Phillip, M., Foght, Julia M., Gray, Murray R., and Dettman, Heather D.

Subjects
Viscosity -- Research, Organosulfur compounds -- Properties, Organosulfur compounds -- Research, Biological sciences
Abstract

The vacuum residue fraction of heavy crudes contributes to the viscosity of these oils. Screening for microbes that can perform this activity is greatly facilitated by the use of newly synthesized compound, bis- (3- pentafluorophenylpropyl)-sulfide (PFPS), as a novel sulfur source.

Published
2004

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