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1. Isolation and characterization of Methanosphaera sp. ISO3-F5, a member of a novel and widespread species of rumen methanogens growing with methanol plus hydrogen

Author

Jeyanathan, Jeyamalar, Palevich, Nikola, Reilly, Kerri, Palevich, Faith P., Maclean, Paul H., Li, Dong, Altermann, Eric, Kim, Caroline C., van Scheepstal, Inge Maartje, Hoskin, Simone O., Kelly, William J., Leahy, Sinead C., Attwood, Graeme T., Ronimus, Ron S., Henderson, Gemma, and Janssen, Peter H.

Published
2024
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2. Crazy good ear candy

Author

Henderson, Gemma, Lawrence, Rhian, and Hutcheson, David

Published
2009

4. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

Author

Seshadri, Rekha, Leahy, Sinead C, Attwood, Graeme T, Teh, Koon Hoong, Lambie, Suzanne C, Cookson, Adrian L, Eloe-Fadrosh, Emiley A, Pavlopoulos, Georgios A, Hadjithomas, Michalis, Varghese, Neha J, Paez-Espino, David, Perry, Rechelle, Henderson, Gemma, Creevey, Christopher J, Terrapon, Nicolas, Lapebie, Pascal, Drula, Elodie, Lombard, Vincent, Rubin, Edward, Kyrpides, Nikos C, Henrissat, Bernard, Woyke, Tanja, Ivanova, Natalia N, and Kelly, William J

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Cancer Genomics, Cancer, Microbiome, Human Genome, Animals, Archaea, Bacteria, Biofuels, Gastrointestinal Microbiome, Humans, Lignin, Microbiota, Rumen, Hungate1000 project collaborators
Abstract

Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B12, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents ∼75% of the genus-level bacterial and archaeal taxa present in the rumen.

Published
2018

6. Complete genome sequence of Methanosphaera sp. ISO3-F5, a rumen methylotrophic methanogen

Author

Palevich, Nikola, primary, Jeyanathan, Jeyamalar, additional, Reilly, Kerri, additional, Palevich, Faith P., additional, Maclean, Paul H., additional, Li, Dong, additional, Altermann, Eric, additional, Kelly, William J., additional, Leahy, Sinead C., additional, Attwood, Graeme T., additional, Ronimus, Ron S., additional, Henderson, Gemma, additional, and Janssen, Peter H., additional

Published
2024
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13. Machine learning predicts and provides insights into milk acidification rates of lactococcus lactis

Author

Karlsen, Signe Tang, Vesth, Tammi Camilla, Oregaard, Gunnar, Poulsen, Vera Kuzina, Lund, Ole, Henderson, Gemma, Bælum, Jacob, Karlsen, Signe Tang, Vesth, Tammi Camilla, Oregaard, Gunnar, Poulsen, Vera Kuzina, Lund, Ole, Henderson, Gemma, and Bælum, Jacob

Abstract

Lactococcus lactis strains are important components in industrial starter cultures for cheese manufacturing. They have many strain-dependent properties, which affect the final product. Here, we explored the use of machine learning to create systematic, high-throughput screening methods for these properties. Fast acidification of milk is such a strain-dependent property. To predict the maximum hourly acidification rate (Vmax), we trained Random Forest (RF) models on four different genomic representations: Presence/absence of gene families, counts of Pfam domains, the 8 nucleotide long subsequences of their DNA (8-mers), and the 9 nucleotide long subsequences of their DNA (9-mers). Vmax was measured at different temperatures, volumes, and in the presence or absence of yeast extract. These conditions were added as features in each RF model. The four models were trained on 257 strains, and the correlation between the measured Vmax and the predicted Vmax was evaluated with Pearson Correlation Coefficients (PC) on a separate dataset of 85 strains. The models all had high PC scores: 0.83 (gene presence/absence model), 0.84 (Pfam domain model), 0.76 (8-mer model), and 0.85 (9-mer model). The models all based their predictions on relevant genetic features and showed consensus on systems for lactose metabolism, degradation of casein, and pH stress response. Each model also predicted a set of features not found by the other models.

Published
2021

15. WIP: Faculty Developer's perceptions of Engineering Instructional Faculty engagement in instructional professional development at HSIs.

Author

Kendall, Meagan R., Perez, Valerie Vanessa Bracho, and Henderson, Gemma

Subjects
ENGINEERING, EDUCATIONAL innovations, CAREER development, MOTIVATION (Psychology), SELF-determination theory
Abstract

This work-in-progress paper details preliminary results from a qualitative study exploring faculty developers' interactions with and perceptions of engineering instructional faculty (EIF) at Hispanic-Serving Institutions (HSIs). One potential resource for supporting EIF's educational innovation efforts is their institutions' center for teaching and learning (CTL). Through CTLs, and similarly named offices, faculty developers provide EIF and other faculty with professional development opportunities, such as pedagogy workshops, consultations, and seminars. By engaging in services provided by faculty developers, EIF can draw on new ideas, energy, and perspectives for instruction that they can incorporate into their beliefs and practices [1]. This is particularly relevant at HSIs, which play a crucial role in enhancing the education of Latinx engineering students. This study aims to understand HSI faculty developers' perceptions of EIF's motivation to participate in professional development programming around instruction. Leveraging the self-determination theory of motivation, our preliminary results suggest that faculty developers recognize how extrinsic and intrinsic factors play an important role in EIF's decisions to engage in instructional development programming. Based on our preliminary results, we encourage the faculty development community to leverage the identity of EIF as problem-solving engineers, identify and correct misconceptions about the role of faculty developers, and be intentional about how their programming responds to the factors intrinsically and extrinsically motivating EIF. [ABSTRACT FROM AUTHOR]

Published
2022

18. Isoflavones and functional foods alter the dominant intestinal microbiota in postmenopausal women

Author

Clavel, Thomas, Fallani, Matteo, Lepage, Patricia, Levenez, Florence, Mathey, Jacinthe, Rochet, Violaine, Serezat, Michele, Sutren, Malene, Henderson, Gemma, Bennetau-Pelissero, Catherine, Tondu, Francoise, Blaut, Michael, Dore, Joel, and Coxam, Veronique

Subjects
Isoflavones -- Health aspects, Functional foods -- Nutritional aspects, Postmenopausal women -- Health aspects, Postmenopausal women -- Food and nutrition, Food/cooking/nutrition
Abstract

Dietary phytoestrogens, such as isoflavones, are used as food additives to prevent menopause-related disorders. In addition to other factors, their bioavailability strongly depends on the activity of intestinal bacteria but the underlying interactions remain poorly understood. A randomized, double-blind, placebo-controlled study was undertaken with 39 postmenopausal women to characterize changes in the dominant microbial communities of the intestinal tract after 2 mo of isoflavone supplementation with and without pro- or prebiotic. The diversity and composition of the dominant microbiota were analyzed by temporal temperature-gradient gel electrophoresis (TTGE) and fluorescent in situ hybridization. Isoflavones alone stimulated dominant microorganisms of the Clostridium coccoides-Eubacterium rectale cluster, Lactobacillus-Enterococcus group, Faecalibacterium prausnitzii subgroup, and Bifidobacterium genus. The stimulation of the Clostridium coccoides-Eubacterium rectale cluster depended on the women's equol excretion and was transient, with the exception of a prolonged bifidogenic effect. Lasting changes in the diversity of the dominant species were also observed. The probiotic strain supplied could be detected by TTGE during its passage through the intestinal tract, and ingestion of fructooligosaccharides triggered a marked and specific bifidogenic effect. In conclusion, this is the first human study that shows changes in the diversity and composition of dominant bacterial communities in response to dietary supplementation with hormone-related compounds combined with functional foods. KEY WORDS: * isoflavone metabolism * intestinal microbiota * functional foods * postmenopausal disorders

Published
2005

25. Co-Designed Research Agenda to Foster Educational Innovation Efforts Within Undergraduate Engineering at HSIs.

Author

Henderson, Gemma, Kendall, Meagan R., Basalo, Ines, and Strong, Alexandra Coso

Abstract

The responsibility to educate and empower underrepresented groups in undergraduate education often relies on the commitment of educators and the curricula they design. Without financial or institutional support, there are limited opportunities for educators from different Hispanic- Serving Institutions (HSIs) to engage in conversations about their curricula developments and share their vision for the future of engineering education. This multi-institutional research project adopted a participatory research design to recognize the existing efforts of educators and foster their curricula and scholarship ideas. A series of three workshops were conducted in 2018 by visiting educators engaged in engineering education at both two and four-year HSIs. Before, during, and after the workshop series, attendees were asked to reflect on three guiding educational philosophies: intrinsic motivation, students as empowered agents, and design thinking. Thirty-six engineering educators from thirteen HSIs from across the Southern United States participated in one of two, two-day workshops where attendees prototyped examples of how they would implement these philosophies at their home institution. Using these prototypes, participants identified the assets they already had and resources they would still need to obtain. Following a thematic analysis of these prototypes from the initial workshops, five themes were identified and prepared for dissemination at the third workshop. Ten participants from the initial workshops attended the final workshop conducted at the 2018 ASEE Annual Conference, and an additional five participants joined as general ASEE Annual Conference attendees. In the final workshop, participants engaged with the preliminary results, further reflected on their progress since the first workshop, and brainstormed research questions they believed the engineering education research community would benefit from answering. The results of this research paper are based on the perspectives of forty-one engineering educators, with a focus on qualitative analysis of questions proposed from fifteen participants at the final workshop. Five research areas emerged: Engineering curricula enhancement, Understanding our students, Faculty development relevant to HSIs, Perceptions of instructional faculty, Long-term impactful approaches. This paper therefore aims to support broader engagement in research and collaboration with and within HSIs, with a goal of increasing the representation of Latinx students in engineering. The results have the potential to target and foster further collaborative scholarly research between educators and promote their curricular efforts in undergraduate engineering education at HSIs. [ABSTRACT FROM AUTHOR]

Published
2019

26. Impact of Faculty DevelopmentWorkshops on Instructional Faculty at Hispanicserving Institutions.

Author

Strong, Alexandra Coso, Kendall, Meagan R., Henderson, Gemma, and Basalo, Ines

Abstract

This research paper will examine the experiences of instructional, non-tenure line (non-tenuretrack/ tenured) faculty at Hispanic-Serving Institutions (HSIs) during and after participation in a multi-institutional faculty development workshop series. As engineering programs increase in size, the demand for instructional, non-tenure track faculty increases. These instructional faculty represent a large percentage, from 25% to over 50%, of the faculty members at both two and four-year institutions. Given their high number of contact hours with engineering students across a curriculum, there exists an opportunity to engage instructional engineering faculty in educational reform and broadening participation efforts. However, research is limited on the effectiveness of different faculty development models for these faculty. Through the analysis of survey data, the findings suggest that the workshop series described in this paper provided a venue for community building among participants and exposure to new techniques and ideas. Overall, this paper makes visible the experiences of these instructional faculty. Specifically, the findings describe how the workshop supported instructional faculty to take strides towards improving the learning experiences of their students. The results have the potential to inform the creation and refinement of faculty development programming at HSIs, within engineering colleges more broadly, and in conjunction with programming created by the American Society for Engineering Education. In addition, the findings will enable further research on this underexplored group within the engineering faculty. [ABSTRACT FROM AUTHOR]

Published
2019

27. Presence of novel, potentially homoacetogenic bacteria in the rumen as determined by analysis of formyltetrahydrofolate synthetase sequences from ruminants

Author

Henderson, Gemma, Naylor, Graham E., Leahy, Sinead C., and Janssen, Peter H.

Subjects
Acetates -- Chemical properties, Cladistic analysis -- Usage, Fatty acids -- Chemical properties, Fermentation -- Analysis, Polymerase chain reaction -- Usage, Rumen -- Microbiology, Rumen -- Research, Biological sciences
Abstract

Sequences of formyltetrahydrofolate synthetase (FTHFS), a key enzyme of the Wood-Ljungdahl pathway was analyzed to survey the presence of rumen homoacetogens which produce acetate from [H.sub.2] and C[O.sub.2]. Sequences that formed 10 clusters containing no known isolates but representing 15% of FTHFS sequences from rumen samples was found to have high HS scores and HoF-HMM matches and hence could represent novel homoacetogens.

Published
2010

28. 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
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32. The Changing Face of Domestic Abuse Service Provision

Author

Henderson, Gemma

Subjects
education, humanities, health care economics and organizations
Abstract

This article aims to explore the changing reality of domestic abuse service provision to victims of domestic abuse in the South West of England. By interviewing the professionals who work with the victims, it explores how cuts to funding is altering provisions for victims and multi-agency working and the realities of the move to tendering via the commissioning process. Results illustrate that austerity measures and government reforms have negatively affected domestic abuse service provision over recent years. Not only are there fewer services available but also changes in social policy are forcing the specialist domestic abuse charities to be replaced by large, generic organisations.

Published
2016

33. Gut-associated denitrification and in vivo emission of nitrous oxide by the earthworm families Megascolecidae and Lumbricidae in New Zealand

Author

Wust, Pia K., Horn, Marcus A., Henderson, Gemma, Janssen, Pater H., Rehm, Bernd H.A., and Drake, Harold L.

Subjects
Earthworms -- Physiological aspects, Nitrous oxide -- Physiological aspects, Intestines -- Microbiology, Intestines -- Research, Biological sciences
Abstract

Four species of earthworms in New Zealand are examined for gut-associated denitrification in order to extend the information base to earthworms in the Southern Hemisphere. The studies have shown that the capacity to emit [N.sub.2]O and [N.sub.2] is a general trait of earthworms and not geographically restricted, and have indicated that species belonging to different earthworm families, Megascolecidae and Lumbricidae, might not have equal capacities to emit [N.sub.2]O.

Published
2009

34. Intestinal bacterial communities that produce active estrogen-like compounds enterodiol and enterolactone in humans

Author

Clavel, Thomas, Dore, Joel, Henderson, Gemma, Blaut, Michael, Alpert, Carl-Alfred, Philippe, Catherine, and Rigottier-Gois, Lionel

Subjects
Estrogen -- Research, Streptococcus -- Research, Streptococcus -- Physiological aspects, Ribosomal RNA -- Research, Biological sciences
Abstract

A study with 24 human subjects was undertaken for the characterization of the bacterial communities responsible for secoisolariciresinol (SECO) activation, that is, the communities that can produce the enterolignans enterodiol (ED) and enterlactone (EL). The intestinal bacteria involved in ED production were part of the dominant microbiota as revealed by most-probable-number enumerations.

Published
2005

37. Human oral isolate Lactobacillus fermentum AGR1487 induces a pro-inflammatory response in germ-free rat colons

Author

Anderson, R.C., Ulluwishewa, Dulantha, Young, Wayne, Ryan, L.J., Henderson, Gemma, Meijerink, Marjolein, Maier, Eva, Wells, J.M., Roy, N.C., Anderson, R.C., Ulluwishewa, Dulantha, Young, Wayne, Ryan, L.J., Henderson, Gemma, Meijerink, Marjolein, Maier, Eva, Wells, J.M., and Roy, N.C.

Abstract

Lactobacilli are thought to be beneficial for human health, with lactobacilli-associated infections being confined to immune-compromised individuals. However, Lactobacillus fermentum AGR1487 negatively affects barrier integrity in vitro so we hypothesized that it caused a pro-inflammatory response in the host. We compared germ-free rats inoculated with AGR1487 to those inoculated with another L. fermentum strain, AGR1485, which does not affect in vitro barrier integrity. We showed that rats inoculated with AGR1487 had more inflammatory cells in their colon, higher levels of inflammatory biomarkers, and increased colonic gene expression of pro-inflammatory pathways. In addition, our in vitro studies showed that AGR1487 had a greater capacity to activate TLR signaling and induce pro-inflammatory cytokines in immune cells. This study indicates the potential of strains of the same species to differentially elicit inflammatory responses in the host and highlights the importance of strain characterization in probiotic approaches to treat inflammatory disorders.

Published
2016

39. The complete genome sequence of the methanogenic archaeon ISO4-H5 provides insights into the methylotrophic lifestyle of a ruminal representative of the Methanomassiliicoccales

Author

Li, Yang, primary, Leahy, Sinead C., additional, Jeyanathan, Jeyamalar, additional, Henderson, Gemma, additional, Cox, Faith, additional, Altermann, Eric, additional, Kelly, William J., additional, Lambie, Suzanne C., additional, Janssen, Peter H., additional, Rakonjac, Jasna, additional, and Attwood, Graeme T., additional

Published
2016
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47. Phylogeny of human intestinal bacteria that activate the dietary lignan secoisolariciresinol diglucoside

Author

Clavel, Thomas, Henderson, Gemma, Engst, Wolfram, Doré, Joël, Blaut, Michael, Unité de recherche d'Écologie et Physiologie du Système Digestif (UEPSD), Institut National de la Recherche Agronomique (INRA), Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Department of Nutritional Toxicology, and German Institute of Human Nutrition

Subjects
[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, PHYLOGENY, INTESTINAL MICROBIOTA, GLUCOSIDE, ENTEROLACTONE
Abstract

International audience; The human intestinal microbiota is essential for the conversion of the dietary lignan secoisolariciresinol diglucoside (SDG) via secoisolariciresinol (SECO) to the enterolignans enterodiol (ED) and enterolactone (EL). However, knowledge of the species that catalyse the underlying reactions is scant. Therefore, we focused our attention on the identification of intestinal bacteria involved in the conversion of SDG. Strains of Bacteroides distasonis, Bacteroides fragilis, Bacteroides ovatus and Clostridium cocleatum, as well as the newly isolated strain Clostridium sp. SDG-Mt85-3Db, deglycosylated SDG. Demethylation of SECO was catalysed by strains of Butyribacterium methylotrophicum, Eubacterium callanderi, Eubacterium limosum and Peptostreptococcus productus. Dehydroxylation of SECO was catalysed by strains of Clostridium scindens and Eggerthella lenta. Finally, the newly isolated strain ED-Mt61/PYG-s6 catalysed the dehydrogenation of ED to EL. The results indicate that the activation of SDG involves phylogenetically diverse bacteria, most of which are members of the dominant human intestinal microbiota.

Published
2006
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