Erika Ganda

Analysis of metagenomic data
Nature Reviews Methods Primers, Liu, Shaopeng, Rodriguez, Judith, Munteanu, Viorel, Ronkowski, Cynthia, Sharma, Nitesh, Alser, Mohammed, Andreace, Francesco, Blekhman, Ran, Błaszczyk, Dagmara, Chikhi, Rayan, Crandall, Keith, Della Libera, Katja, Francis, Dallace, Frolova, Alina, Gancz, Abigail, Huntley, Naomi, Jaiswal, Pooja, Kosciolek, Tomasz, Łabaj, Pawel, Łabaj, Wojciech, Luan, Tu, Mason, Christopher, Moustafa, Ahmed, Muralidharan, Harihara, Mutlu, Onur, Ghiasi, Nika, Rahnavard, Ali, Sun, Fengzhu, Tian, Shuchang, Tierney, Braden, Van Syoc, Emily, Vicedomini, Riccardo, Zackular, Joseph, Zelikovsky, Alex, Zielińska, Kinga, Ganda, Erika, Davenport, E, Pop, Mihai, Koslicki, D, Mangul, Serghei, 2025

Antimicrobial Resistance and Zoonotic Potential of Nontyphoidal Salmonella From Household Dogs
Zoonoses and Public Health, Kenney, Sophia M., M'ikanatha, Nkuchia M., Ganda, Erika, 2025

Corrigendum: Use of intrauterine dextrose as an alternative to systemic antibiotics for treatment of clinical metritis in dairy cattle: a microbiome perspective (Frontiers in Veterinary Science, (2024), 11, (1478288), 10.3389/fvets.2024.1478288)
Frontiers in Veterinary Science, Lection, Jennine, Van Syoc, Emily, Miles, Asha, Hamilton, Julia, Martinez, Marcela, Bas, Santiago, Silverman, Justin, Barragan, Adrian, Ganda, Erika, 2025

A comparative study of the bacterial diversity and composition of nursery piglets’ oral fluid, feces, and housing environment
Scientific Reports, Buiatte, Vinicius, Fonseca, Ana, Alonso Madureira, Paloma, Nakashima Vaz, Andréia Cristina, Tizioto, Polyana Cristine, Centola Vidal, Ana Maria, Ganda, Erika, de Azevedo Ruiz, Vera Letticie, 2024

Development and evaluation of statistical and artificial intelligence approaches with microbial shotgun metagenomics data as an untargeted screening tool for use in food production
mSystems, Beck, Kristen L., Haiminen, Niina, Agarwal, Akshay, Carrieri, Anna Paola, Madgwick, Matthew, Kelly, Jennifer, Pylro, Victor, Kawas, Ban, Wiedmann, Martin, Ganda, Erika, 2024

Identifying knowledge gaps surrounding antimicrobial resistance: An exploratory study of antimicrobial resistant genes on Pennsylvania dairy farms
Journal of Rural Studies, Ransom, Elizabeth, Bierly, Stephanie, Ganda, Erika, 2024

Whole-genome sequencing of three ciprofloxacin-resistant Salmonella Reading (ST93) strains, an emerging Salmonella serovar in the poultry sector of Pakistan
Genome Announcements, Siddique, Abubakar, Tauqeer, Azka, Ali, Amjad, Ahsan, Aitezaz, Iqbal, Sajid, Patel, Ami, Moore, Terence, Ganda, Erika, Rahman, Abdur, 2024

Comparative genomic analysis of Brazilian Mesomycoplasma ovipneumoniae strains revealed genomic differences associated with the geographic origin and health status and mutations in the gyrA
Veterinary Microbiology, Gaeta, N. C., de Sá Guimarães, A. M., Timenetsky, J., Clouser, S., Gregory, L., Ganda, E., 2024

Changes in the type 2 diabetes gut mycobiome associate with metformin treatment across populations
mBio, Van Syoc, Emily, Nixon, Michelle, Silverman, Justin, Lou, Yuhong, Luo, Yuhong, Gonzalez, Frank, Elbere, Ilze, Klovins, Janis, Patterson, Andrew D., Rogers, Connie, Ganda, Erika, 2024

Investigating antibiotic free feed additives for growth promotion in poultry: effects on performance and microbiota
Poultry Science, Fonseca, A, Fonesca, Ana, Kenney, Sophia, Van Syoc, Emily, Bierly, Stephanie, Dini Andreote, F, Dini-Andreote, Francisco, Silverman, Justin, Boney, J, Ganda, Erika, 2024

The Effects of Bifidobacterium Probiotic Supplementation on Blood Glucose: A Systematic Review and Meta-Analysis of Animal Models and Clinical Evidence
Advances in nutrition (Bethesda, Md.), Van Syoc, Emily P., Damani, Janhavi, DiMattia, Zachary, Ganda, Erika, Rogers, Connie J., 2024

Editorial: Foodborne bacterial pathogens under the One Health perspective - antimicrobial resistance, epidemiology, virulence, and zoonotic impact
Frontiers in cellular and infection microbiology, de Oliveira, Laura Maria Andrade, Ribeiro, Rachel Leite, Ganda, Erika, 2024

Seroprevalence and risk factors for brucellosis amongst livestock and humans in a multi-herd ranch system in Kagera, Tanzania
Frontiers in Public Health, Hudson, Peter, Lyimo, Beatus, Hugho, Ephrasia, Mathew, Coletha, Mayenga, Charles, Lukambagire, Abdul Hamid, Lyimo, Samson, Munuo, Lidia, Byukusenge, Maurice, Withall, Jodie, Ashford, Roland T., Mmbaga, Blandina T., Makondo, Zachariah, McGiven, John, Radzio-Basu, Jessica, Ganda, Erika, Middlebrook, Earl A., Bartlow, Andrew W., Fair, Jeanne M., Shirima, Gabriel, Sriranganathan, Nammalwar, Kazwala, Rudovick R., Cattadori, Isabella M., Kapur, Vivek, Buza, Joram J., Katani, Robab, 2024

Alterations of rumen and fecal microbiome in growing beef and dairy steers fed rumen-protected Capsicum oleoresin
Journal of Animal Science, Bierly, S, Van Syoc, E, Westphalen, M, Miles, A, Gaeta, N, Felix, Tara L., Hristov, Alexander, Ganda, Erika, 2024

Use of intrauterine dextrose as an alternative to systemic antibiotics for treatment of clinical metritis in dairy cattle: a microbiome perspective
Frontiers in Veterinary Science, Lection, Jennine, Van Syoc, Emily, Miles, Asha, Hamilton, Julia, Martinez, Marcela, Bas, Santiago, Silverman, Justin, Barragan, Adrian, Ganda, Erika, 2024

The bovine foot skin microbiota is associated with host genotype and the development of infectious digital dermatitis lesions
Microbiome, Bay, V., Gillespie, A., Ganda, E., Evans, N. J., Carter, S. D., Lenzi, L., Lucaci, A., Haldenby, S., Barden, M., Griffiths, B. E., Sánchez-Molano, E., Bicalho, R., Banos, G., Darby, A., Oikonomou, G., 2023

Saccharomyces cerevisiae fermentation product improves robustness of equine gut microbiome upon stress
Frontiers in Veterinary Science, Ganda, Erika, Chakrabarti, Anirikh, Sardi, Maria I., Tench, Melissa, Kozlowicz, Briana K., Norton, Sharon A., Warren, Lori K., Khafipour, Ehsan, 2023

The association of hyperketonemia with fecal and rumen microbiota at time of diagnosis in a case-control cohort of early lactation cows
BMC Veterinary Research, Miles, Asha M., McArt, Jessica A.A., Lima, Svetlana F., Neves, Rafael C., Ganda, Erika, 2022

Metformin modulates the gut microbiome in broiler breeder hens
Frontiers in Physiology, Van Syoc, E, Weaver, E, Rogers, Connie Jo, Silverman, Justin, Ramachandran, Ramesh, Ganda, Erika, 2022

Effect of Intramammary Dry Cow Antimicrobial Treatment on Fresh Cow’s Milk Microbiota in California Commercial Dairies
Antibiotics, Basbas, Carl, Aly, Sharif, Okello, Emmanuel, Karle, Betsy M., Lehenbauer, Terry, Williams, Deniece, Ganda, Erika, Wiedmann, Martin, Pereira, Richard V., 2022

Draft genome sequences of 25 Salmonella enterica serovar Agona strains isolated from poultry and associated food products harbouring multiple antibiotic resistance genes
Journal of Global Antimicrobial Resistance, Siddique, Abubakar, Ullah, Nimat, Ali, Amjad, Patel, Ami, Moore, Terence, Kenney, Sophia M., Ganda, Erika, Rahman, Abdur, 2022

Global metagenomics analyses demonstrate metformin-induced changes in the gut mycobiome in subjects with type 2 diabetes
FASEB Journal, Van Syoc, Emily, Rogers, Connie J., Ganda, Erika, 2022

The first Mycoplasma ovipneumoniae recovered from a sheep with respiratory disease in Brazil – draft genome and genomic analysis
Veterinary Research Communications, Gaeta, Natália C., de Sá Guimarães, Ana Marcia, Timenetsky, Jorge, Clouser, Stephanie, Gregory, Lilian, Ganda, Erika, 2022

Lactobacillus reuteri and enterococcus faecium from poultry gut reduce mucin adhesion and biofilm formation of cephalosporin and fluoroquinolone-resistant salmonella enterica
Animals, Siddique, Abubakar, Azim, Sara, Ali, Amjad, Adnan, Fazal, Arif, Maryum, Imran, Muhammad, Ganda, Erika, Rahman, Abdur, 2021

DNA extraction and host depletion methods significantly impact and potentially bias bacterial detection in a biological fluid
mSystems, Ganda, Erika, Beck, Kristen, Haiminen, Niina, Silverman, J, Kawas, Ban, Cronk, Brittany, Anderson, Renee, Goodman, Laura, Wiedmann, Martin, 2021

Choice of commercial dna extraction method does not affect 16s sequencing outcomes in cloacal swabs
Animals, Van Syoc, Emily, Carrillo Gaeta, Natália, Ganda, Erika, 2021

Maternal influences on oral and faecal microbiota maturation in neonatal calves in beef and dairy production systems
Animal Microbiome, Barden, Matthew, Richards-Rios, Peter, Ganda, Erika, Lenzi, Luca, Eccles, Richard, Neary, Joseph, Oultram, Joanne, Oikonomou, Georgios, 2020

A Cross-Sectional Study of Dairy Cattle Metagenomes Reveals Increased Antimicrobial Resistance in Animals Farmed in a Heavy Metal Contaminated Environment
Frontiers in Microbiology, Gaeta, Natalia Carrillo, Bean, Emily, Miles, Asha Marie, Carvalho, Daniel Ubriaco Oliveira Gonçalves de, Alemán, Mario Augusto Reyes, Carvalho, Jeferson Silva, Gregory, Lilian, Ganda, Erika, 2020

Complex Interactions Between Weather, and Microbial and Physicochemical Water Quality Impact the Likelihood of Detecting Foodborne Pathogens in Agricultural Water
Frontiers in Microbiology, Weller, Daniel, Brassill, Natalie, Rock, Channah, Ivanek, Renata, Mudrak, Erika, Roof, Sherry, Ganda, Erika, Wiedmann, Martin, 2020

The microbiome of Escherichia coli and culture-negative nonsevere clinical mastitis: Characterization and associations with linear score and milk production
Journal of Dairy Science, Vasquez, A. K., Ganda, E. K., Capel, M. B., Eicker, S., Virkler, P. D., Bicalho, R. C., Nydam, D. V., 2019

Effects of pegbovigrastim administration on periparturient diseases, milk production, and reproductive performance of Holstein cows
Journal of Dairy Science, Zinicola, M., Korzec, H., Teixeira, A. G.V., Ganda, E. K., Bringhenti, L., Tomazi, A. C.C.H., Gilbert, R. O., Bicalho, R. C., 2018

Normal milk microbiome is reestablished following experimental infection with Escherichia coli independent of intramammary antibiotic treatment with a third-generation cephalosporin in bovines
Microbiome, Ganda, Erika K., Gaeta, Natalia, Sipka, Anja, Pomeroy, Brianna, Oikonomou, Georgios, Schukken, Ynte H., Bicalho, Rodrigo C., 2017

The bovine colostrum microbiome and its association with clinical mastitis
Journal of Dairy Science, Lima, Svetlana F., Teixeira, Andre G.V., Lima, Fabio S., Ganda, Erika K., Higgins, Catherine H., Oikonomou, Georgios, Bicalho, Rodrigo C., 2017

A metataxonomic approach could be considered for cattle clinical mastitis diagnostics
Frontiers in Veterinary Science, Oultram, Joanne W.H., Ganda, Erika K., Boulding, Sarah C., Bicalho, Rodrigo C., Oikonomou, Georgios, 2017

Deciphering upper respiratory tract microbiota complexity in healthy calves and calves that develop respiratory disease using shotgun metagenomics
Journal of Dairy Science, Gaeta, Natália C., Lima, Svetlana F., Teixeira, Andre G., Ganda, Erika K., Oikonomou, Georgios, Gregory, Lilian, Bicalho, Rodrigo C., 2017

Longitudinal metagenomic profiling of bovine milk to assess the impact of intramammary treatment using a third-generation cephalosporin
Scientific Reports, Ganda, Erika K., Bisinotto, Rafael S., Lima, Svetlana F., Kronauer, Kristina, Decter, Dean H., Oikonomou, Georgios, Schukken, Ynte H., Bicalho, Rodrigo C., 2016

Effects of injectable trace mineral supplementation in lactating dairy cows with elevated somatic cell counts
Journal of Dairy Science, Ganda, E. K., Bisinotto, R. S., Vasquez, A. K., Teixeira, A. G.V., Machado, V. S., Foditsch, C., Bicalho, M., Lima, F. S., Stephens, L., Gomes, M. S., Dias, J. M., Bicalho, R. C., 2016

Evaluation of an on-farm culture system (Accumast) for fast identification of milk pathogens associated with clinical mastitis in dairy cows
PLoS One, Ganda, Erika Korzune, Bisinotto, Rafael Sisconeto, Decter, Dean Harrison, Bicalho, Rodrigo Carvalho, 2016

Associations among Trueperella pyogenes, endometritis diagnosis, and pregnancy outcomes in dairy cows
Theriogenology, Bicalho, M. L.S., Lima, F. S., Machado, V. S., Meira, E. B., Ganda, E. K., Foditsch, C., Bicalho, R. C., Gilbert, R. O., 2016

Lameness prevalence and risk factors in large dairy farms in upstate New York. Model development for the prediction of claw horn disruption lesions
PLoS One, Foditsch, Carla, Oikonomou, Georgios, Machado, Vinícius Silva, Bicalho, Marcela Luccas, Ganda, Erika Korzune, Lima, Svetlana Ferreira, Rossi, Rodolfo, Ribeiro, Bruno Leonardo, Kussler, Arieli, Bicalho, Rodrigo Carvalho, 2016

Oral administration of Faecalibacterium prausnitzii decreased the incidence of severe diarrhea and related mortality rate and increased weight gain in preweaned dairy heifers
PLoS One, Foditsch, Carla, Van Vleck Pereira, Richard, Ganda, Erika Korzune, Gomez, Marilia Souza, Marques, Eduardo Carvalho, Santin, Thiago, Bicalho, Rodrigo Carvalho, 2015

The effect of intrauterine infusion of dextrose on clinical endometritis cure rate and reproductive performance of dairy cows
Journal of Dairy Science, Machado, V. S., Oikonomou, G., Ganda, E. K., Stephens, L., Milhomem, M., Freitas, G. L., Zinicola, M., Pearson, J., Wieland, M., Guard, C., Gilbert, R. O., Bicalho, R. C., 2015

Prepartum and postpartum rumen fluid microbiomes: Characterization and correlation with production traits in dairy cows
Applied and Environmental Microbiology, Lima, Fabio S., Oikonomou, Georgios, Lima, Svetlana F., Bicalho, Marcela L.S., Ganda, Erika K., de Oliveira Filho, Jose C., Lorenzo, Gustavo, Trojacanec, Plamen, Bicalho, Rodrigo C., 2015

The use of next generation sequencing of the 16s rRNA gene in dairy cattle mastitis diagnostics
Cattle Practice, Oikonomou, G., Boulding, S., Ganda, Erika, Bicalho, R. C., 2015